The problem is that some plugins need more information storage. There are two solutions:

1/ either add new table such as enrol_self which joins the current enrol table - easier to implement, better for performance, 100% BC
2/ deprecate custom fields in enrol table and start creating extra tables for each enrol plugin that contains instance info - cleaner solution, major backwards compatibility problems, caching problems

Historically I implemented 1/ during the migration from 1.9 because I wanted to move the enrol info away from course table and this was the safest way. At that time it also significantly helped with performance because the core can prefetch the enrol instance records and pass them around.

I have discussed this with Eloy and I guess we agree that we should do 1/ now and delay the decision for 2/ later.