Some of the paint will scratch off the plastic in an environment where it's subjected to abrasion, but I find that it works well enough for my purposes. For the things that get the most handling, and where immediate prominent visibility is essential, I have done a touch up from time to time, but it never got anywhere near to "disappearing".
For one thing, convenience. I just want to quickly mark the connectors. I can't imagine an acrylic paint option would provide so much convenience.
As for technical differences, I don't know. I've been happy with the markers, so found no need to go looking at other alternatives. You can compare the two if you like. I can tell you that the paint in the markers is solvent-based. They are pretty stinky. I haven't had any problem with them drying out, despite them being years old.
I'm very interested in your findings as well as any approaches taken by others.
In a previous discussion on this subject, someone mentioned that they use "White-out" correction fluid. I happened to have a bottle on hand so I did a comparison and found that the paint marker's paint was a little bit more durable than the white-out.
I use dollar-store nail polish for a very long time. It is rugged, dries hard and quickly with a hair dryer (or hot air from soldering station.) I use a tooth-pick to apply.
I use Testors red model paint (if you can still find it). My local Ace Hardware store still carries a limited number of colors.
I like it better than the markers and nail polish. Using a fine brush I can easily put small red dots and color the base of a dupont.
Regards to the colored terminals i allready have these and all are green or blue. I want to mark each terminal with black and red for negative and positive. For the 3-pin terminals i also want to color yellow or blue for signal lines etc.