Here's what I just tried:

Changed the repeats to 1 (from 3) for all the transport commands in SageTV Smart Macro group on the MSC-400. This is the only place I can see where one can change this.

Modified my activity to trigger these smart macros from the transport buttons.

With the IR output POT for the SageTV port all the way counter-clockwise, this produced the most lag. I had to back the pot off a bit because if turned firmly all the way, it simply didn't work at all.

With the IR output POT turned all the way clockwise, this produced the least amount of lag.

While it's not monumental, it's easy enough to tell the difference between full clockwise and full counter-clockwise on the output. I'm assuming counter-clockwise reduced the output, even though this isn't mentioned in the documentation specifically.

There's a side-benefit to having the audible interference I previously mentioned. I can hear when the MSC-400 starts doing something with the signal and compare...

With the triggers on their most laggy (counter-clockwise IR output adjustment), I can hear noise, then a noticeable delay before SageTV registers anything. With the least amount of lag, that delay is smaller. But there's still an unresponsiveness when letting the button go after holding it down for a bit that's not there when doing straight IR. Seems like a half second at least, which with quick repeats means you won't be able to stop where you'd expect to when skipping.

When doing straight IR via the MSC-400's simple IR routing (IR input port which blasts IR out to all ports), there really are no perceivable delays. I can hear the interference noise and immediately SageTV responds. I need to note that with full counter-clockwise, even backed off a hair, straight IR relay doesn't work. The IR output must be turned up somewhat more for relaying to work reliably.

I repeated the tests with additional buttons, including the 4 direction buttons. It shows that this method is not usable at all, as the perceived legginess when navigating the UI is even worse than when using the transport controls. There are definitely two stages to the lag.

Pressing a button on the MX-980 for a trigger reacts slowly. You can see that the RF LED on the receiver does not light up until a split second after the button has been fully depressed. This is confirmed with the audible interference on my pre-amp which happens immediately when that LED lights up. Then SageTV doesn't respond for another split second, all together making it very awkward to use.

It's also impossible to quickly press a button multiple times as the MX-980 and MSC-400 will not respond fast enough. For instance, pressing UP three times very quickly will only register a single UP in SageTV. It seems that the MX-980 picks up two presses, but the MSC-400 only one.

Using the serial connection on my pre-amp, the MSC-400 seems to be able to pick up both of the MX-980's transmissions - again, even though I'm pressing the button 3 times.

While it's not as responsive as I'd prefer, at least the MX-980 doesn't buffer all the presses like some other products do and then spit them back in slow motion in what seems like a never-ending loop (Harmony remotes for example, yuck).