InDesign's QR encoder has remained on the "handy, useful, imperfect" border of things, and unless a recent update changed this, it encoded in 2.1 unless a workaround such as you're using was applied. There were changes recently, but I can't remember if an update to 3.0 was part of it.
If you have demanding needs from QR, use another generator, one with more control and interactive settings. The one in ID is a convenience that doesn't really meet all needs.
╟─ Word & InDesign to Kindle & EPUB: a Guide to Pro Results (Amazon) ─╢