The overstay rules came into effect I believe 20 March 2016. You seem to have exited the country June 2016, after a 4 year overstay, which would indicate a 5 year ban. If I am reading the stamps correctly.
Ideally they want people on extensions because they can exert better control, and they do have more stringent requirements, the non B class in particular.
Bottom line is they want to thin the herd so to say, or get them on Elite Visas (where you cannot work anyways, which is idiotic).
I don't disagree with everything you have said though.
is saying: " Such a visa holder is required to exit every 90 days."
No, such a visa holder is required to do multiple business visits to Thailand for a maximum of 90 days per visit (underline the word visit), not to continuously stay 360 days with visa runs in between.
The fact that people do it and it's all been good so far is a different story.
Right ok so you don't have a one year visa. You applied initially for a 3 month single entry non ED visa at an overseas consulate. Your permission of stay has been extended a few times since then by receiving 3 month extensions of stay. After a certain number of extensions, roughly totalling 8 months, Immigration will not extend further. Then you have to restart the process by applying for another single entry non ED overseas, and go to Level 2 of studies.
In 3 years looking at multiple forums i have not seen a report of a non B issued in Bali. They are however likely to follow Jakarta for their requirements, and according to Jakarta, they would ask for evidence of qualification (university certificates and CV).
You could pay them a visit if you happen to be there and see what they say if it suits you, but I would expect them to be more demanding than Malaysia.