I've been looking at this further and I think the answer is relatively simple, although I wish they'd update the app to better handle this if my understanding is confirmed.
As I noted above I couldn't get the smoke on and smoke off buttons on the iCab app's SPEED screen to work. Circled in red below.
This was with my LionMaster TMCC UP Challenger. However, I had the same issue with my TMCC Mo-Pac RS11. I don't yet have a Legacy engine to test with, but I suspect the buttons on the iCab app I've circled will only work for a Legacy engine. That they aren't greyed out if this is indeed the case would seem an unfortunate oversight since the app clearly knows it's dealing with a TMCC engine and not a Legacy engine (see top of the app screen "83: TMCC Engine").
Every control system (TMCC, Legacy, DCS, DCC) has quirks, so my more pressing question was whether I could get iCab to control the smoke units in these TMCC engines at all. And it turns out you can.
The touch screen on the Cab2 changes icons based on what you're controlling (the TMCC smoke control buttons are a "-" and "+") but if you go back to the Cab1 all you had was the numeric keypad and the clear plastic overlays to tell you what a given engine would do with a given keypad number button once AUX1 was pressed. It turns out you just need to go back to looking at it that way with iCab.
By changing to the PGM screen on iCab (above) you can press the AUX1 button and then select the old numeric control number (in this case 8 for smoke off and 9 for smoke on). You can get AUX1 to "latch" (as shown above) and in that case the screen functions pretty much like a Cab1 would after you press AUX1 on that handheld. (The AUX1 would be "in effect" for every number on the keypad you then pressed until you preceded the number with a different control button like TR, ENG, AUX2 etc.) The difference I saw was that even with AUX1 "latched" on the iCab, you couldn't hold your finger on the "9" key and get the smoke boost you get holding that key down on the Cab1. The iCab app only sends the command one time in the above scenario. So you have to rapidly tap on the "9" to get the same result as just holding down on the Cab1 (or Cab2).
I think some slight code modifications would enhance the intuitiveness of the iCab app relative to smoke unit control specifically (and AUX1 controls for TMCC engines in general). If the smoke icons on the iCab SPEED screen only work with Legacy locos then grey them out if the engine being controlled is TMCC. Better yet, why not make pressing the AUX1 on the PGM screen change the keys to the same symbols that would be displayed on the Cab2? You have to have the 990 to use LCS to control Lionel locos anyway so why not make some things more consistent between Cab2 and iCab? (There are some things that were changed that were for the better though. For instance, I notice that powering off a track controlled by a TPC was AUX1 then "0" on the Cab2 where on the iCab it's just the "Reset" button on the TR screen. So even though it's not consistent it's more intuitive.)