I have a similar setup to what you have Planned. I feel your pain as I did not have much support for my setup and mostly had to figure things out through trial and error. To quickly answer your questions - No, there isn't 1 remote or 1 app that will control all of this. If you see an advertisement saying there is they are lying. If they're telling the truth please let me know.

I will describe my setup and tell you how I control it, what has worked and what has failed.

My Setup:
3 wall mounted TVs. A 60" LG TV and 2 identical 40" Sony Smart TVs

The TVs are connected into a HTD Lync 12 Whole House Audio system through a optical audio switcher that has a remote control.

My setup is mainly for watching sports games and I like to easily be able to switch audio to the game I want listen to. I also have an electric fireplace, HTPC, Video game consoles, Sonos Connect, IP surveillance cameras, Wifi thermostat, and remote lighting.

My first attempt at controlling everything was to go out and buy the Harmony Ultimate Home Hub Remote. All my devices were "compatible" using their online checker and it sounded perfect. For multiple reasons the Harmony Ultimate Home was not very useful and user friendly for my setup. If you're interested in my indepth opinion on this remote you can read my review of Amazon.com - user name FullyCompletely.

Long story short is that Harmony hub uses IR to control Smart TVs and it doesn't detect multiple identical TVs by their IP address as I expected. It treats identical TVs as a single TV. All identical TVs will receive the remote commands and mirror each other. Sometimes this is cool but not always.

Fortunately I purchased Sony Smart TVs that have a very useful Android app called "TV SideView". The app detects compatible TVs on your home network. From inside this app I can control my TVs independently and I can actually access streaming services and SmartTV features much faster than using any remote.

I've returned my Harmony Ultimate Home remote and now I use a tablet dedicated to my TV and I use a $25 Sony Universal Learning remote to control all my "non connected" IR devices.

I'm able to control my Smart TVs and audio system with my tablet using their native android apps. At first I didn't consider this method of control because I didn't want to use multiple devices and multiple apps because it seemed tedious and inconvenient. In reality the tablet is actually much easier to navigate than the small harmony LCD screen was. The free Android apps that my devices are designed to work with offer full feature support. Harmony will call your devices compatible but may have limited support. So no matter what I always needed a Smartphone/Tablet to achieve the control I wanted. I can actually use my basic universal remote a lot faster than the Harmony remote because it has a lot more programmable buttons. But I get no fancy complex automaton with my setup. Which I will gladly go without for quicker and full feature control. Harmony activity automaton doesn't work very well for multiple TV setups. I explain why I think this in my amazon review.

I can still achieve independent control of my identical TVs with my universal IR remote by using a little trickery. I have an IR Receiver connected to only 1 of the identical TVs and the IR Receiver runs from the back of the TV inside the wall - down to the basement - and up back into my room on the wall beside my couch

How I achieve independent IR control:
I point my remote at the TVs mounted on the wall and they both follow along with remote commands. When I get the TVs displaying the content I want I then move on to changing only one TV by pointing my remote directly at the IR receiver beside my couch. Since an IR signal is a "line-of-sight" type of signal it never reaches the other TV. I'm sure this is not the only way of doing this but it's probably the cheapest and quickest as it doesn't require any switching of sources on your remote or waiting for apps to load.

My universal remote can control my HTPC and XBMC/kodi Media Center. The Sony TV SideView app can actually detect the XBMC/Kodi Server so I can view any local computer video on any TV simultaneously. I could never do this with only a Harmony Remote or with 1 single "control everything" app. But I wish I could!

I can't vouch for how this setup works with a cable TV subscription because I don't have one. But the SmartTV app asks for your Postal Code/Zip Code and detects local service providers and allows you to add and edit channels. So I believe independent control would be possible for a cable setup with a tablet and with a universal remote.

I watch Sports with a HTPC and with apps built into my Smart TVs. I stream additional content to the TVs with servers that I can control with apps on a tablet. I also have each TV connected to the same computer's video card which gives me the flexibility of a multi display computer.

I've considered using a home control remote builder like iRule but since monthly fees are against my religion I haven't been able to make the leap to iRule.

Someone recommended to hire a professional, iRule is probably similar to what a professional would offer. I met with a professional that was offered to me through my home builder. Had I went with the professionals I would be broke and have a system that can't really be changed or upgraded without asking/paying them for help.

Like Harmony Ultimate Home I suspect services like iRule have limited Support. You'd have access to a lot more features by simply using a tablet with free/cheap apps, a decent universal remote, and a keyboard/mouse to take full advantage of your HTPC.

My setup and methods of control are not perfect. It lacks automation, it takes practice. It takes time to learn
There's no crash course on how to make everything work like you might get from a professional installer. Strangers can't walk in and know how to control it like their home cable boxes; Which has its advantages because some people feel entitled to take over your entertainment system.

My wife can use everything just fine. She's impatient and rarely has had any complaints since "HOW COULD YOU SPEND $300 ON A [Harmony Ultimate Home] REMOTE!?"