There is no one right way on how to exit the MTS when going for a MTSISB. One way might be better depending on a few things.
Yes you need to end the MTS right as you're on the spot where the machine briefly catches air. The A button needs to be held down until the machine 'lands' back on the ground. If you want to MT right after a MTSISB, if you let go of the A button too early after exiting the MTS, you won't get the shift boost despite getting the appropiate amount of lift off from the ground. It is much better to hold A for longer than necessary since at least you will get the shift boost, then from there you can reduce the duration of the A button press.
As for memorization vs feel, I guess it's both. You need to get a feel for the timing by practicing. But what helps get you that timing is with a consistent set up that deviates very little from attempt to attempt, especially with more difficult to exectue shift boosts like the one in Aero Dive.
For OSMS, it is very easy to get too much air for going too fast for the position your machine is at. That would mean positining your machine more to the left to get the MTSISB at those higher speeds
For ADS, the faster you're going the more to the left you want to be. But you can go too fast no matter where you go for the shift boost. So you will intentionally either delay the MTS or intentionally do a slower MTS (by holding both L and R or using less steering input).
Here's a video that shows the inputs as I do consecutive MTSISBs in Twist Road: https://youtu.be/bHq3Tvb2M10?t=1m4s