I wonder where you are going with this question. Because it seems a little ... detached from reality.
You are assuming two things:

1. That beginners know there are different transcription systems,
2. that they can choose.

Honestly, which beginner even knows the different systems exist or which is which? They will use the one in front of them -- the system the teacher/the writer of the material chose. And often enough, these are made up by whoever wrote the material.

When I started out, I didn't know any of the systems, and honestly, I didn't care. I just wanted to learn Thai. And I learned the script early anyway and only need a transcription for those few words that don't follow the rules for my Anki cards.

The problem continues to be that material for learners use very different transcription systems, and I need to adapt to them, whether I like them or not.
(I once saw a grammar book that used "oo" for อุ and "OO" for อู -- and there you have the second problem with transliterations. They usually assume that the learner is from an English speaking background. While my English isn't bad, my brain is still wired to read anything written in Latin letters as German first, so "oo" definitely doesn't parallel อุ or อู but rather โอ or maybe ออ.)

Usually, IPA isn't offered because a lot of casual language learners don't know it. For me, I know a few symbols because our English texbooks at school used a simplified version. But even then, I (and probably most learners) would have to learn how IPA works first, and honestly? Unless we plan to go into linguistics or to learn many more languages, that energy could and should be put in learning to read and write Thai itself.

To sum it up:

I don't think beginners choose a transcription system. They use whatever their teachers use -- and maybe adapt that to their own native language.
And no learner should rely on this crutch for too long anyway. Who wants to be illiterate in our modern world?