Should S3&K be timed in real time?

So over the past little while I've been playing Sonic 3 & Knuckles again I've been giving serious thought to changing the timing of the game to real time. In-game time has worked for quite some years now but I'm beginning to think there are too many issues that it just doesn't resolve. In order from most to least intrusive:
* Pausing. Using purely the game timer lets you pause for free to line up tricks. I would still do this when the situation called for it, of course, because not using the tricks at all is a far greater loss, but it might encourage me to learn methods for some tricks that don't involve a pause.
* At the end of each act 1, you can keep the signpost juggling for as long as you want, or (more relevantly for a speedrun) until it's going to land on an item you need. In the case of Mushroom Hill, where Sonic gets the lightning shield (the only such use of this in the run currently), this is a really hard shot as it's right up against the left wall, and gets even harder now that Tails can get in the way. This can take upwards of 30 seconds to get, and it doesn't count against you at all. This has always felt kind of wrong to me.
* The in-game timer only tracks down to the second, and therefore is not truly accurate. Real time fixes this.
* It would resolve one particular edge-case that in-game timing has always had but kind of shied away from - for a Knuckles run, by strict game time it would be faster to go through Sonic's boss rush in Launch Base 2, but by real time it is over a minute slower. We've always just gone Knuckles's way by convention, as when I first brought it up at SDA they said they would add the time spent in the boss fights on the platform (where the timer doesn't restart, which is the only reason it's faster in the first place!), which by itself made it not worth doing.

Weighed against all of that is the classic reasoning for timing Sonic games in game time: the incentive to play stages badly to save time. In particular, an optimal Sky Sanctuary for real time would look really strange - you would simply stand next to the teleporter for 3-4 seconds before going up to the boss fight. Carnival Night 1 and Hydrocity 1 have similar issues but their boss fights are much more variable and unpredictable.

While thinking about this for the umpteenth time last night, the Old El Paso girl drifted into my head and delivered her clarion cry: "Why not both?"

My proposal: S3&K runs going forward should be timed in real time, but with the frames where bonuses are being tallied removed. Conveniently, this is really easy to figure out because the amount of frames each bonus screen will be counting is displayed on the screen! Whichever of the two bonuses is larger, remove the last two zeroes and you're done - because the game counts down 100 points every frame.

This means:
* No incentive to slow down during the stage
* Pausing will count against you
* Time will be a more accurate record of time spent in the stage
* Knuckles runs no longer have that question mark hanging over them
* Should not adversely affect runs done prior to this change (of which there aren't too many anyway)

The only real drawback is the extra factor you have to consider in timing, but classic Sonic has always had a bit of a barrier up because of that anyway with IGT. The number of frames itself could be easily tracked - perhaps as something that pops up when you start a run in Livesplit, like IGT does now. Or you could just adjust it after completing a run. As a verifier I'd probably find myself doing that for new runs that came in anyway.

Let me know your thoughts!
~mike89