Transforming offstage is actually never a safe idea because of random load time factor. You can wind up falling farther than anticipated. If you want to recover using Transform anyway, it's better to use Sheik's 2nd jump and immediately roll to Transform input. Then C-stick towards the stage so Zelda buffers a kick in that direction which allows her to get aerial momentum and can then UpB. Doing the Transform recovery correctly is the first step, hoping that it works.
Transforming high above the stage and falling downwards is again, subject to randomness and not solicited even with the default mechanic. The default mechanic allows a pursuer to just wait for you to come out of the Transform, the lagless one still puts the pursuer at a risk due to Zelda's effective aerials, and that air dodges are not quick enough to react to. By using Transform on the ground, you have access to shielding, which is possible on frame 1.
As another addendum as to why not much of this is actually true is because of the actual vulnerable times. Zelda's and Sheik's Transform times outside of loading are very slightly different, but we'll use 36 to start, 30 endlag as an average.
Normal: 36 start up -> random loading -> 30 endlag
Modified: 80 start up -> random loading -> 0 endlag
The amount of time for the enemy to actually get to you is negligibly different. The only difference is that, you will be able to Transform more often with the normal mechanic because it gets to the loading faster, but as far as actually being punished for it, it's still in favor of a lagless one. Where you get the idea that the modified one was ever more punishable except in cases where it wasn't a good idea to use to begin with is strange enough.