You should approach "your" CAA with that question.
Each country does interpret the EASA rules a bit different. Yes, I know, this is not what was meant by uniform approach, but there are enough buttheads and some few just defending their local chairs. Some countries will treat CBIR als a fully fledged alternate route to IR, but there are some countries trying to push the CB approach to "PPL only", in which case your ATPL'ish path would be no option. Reality usually is somewhere in between.
Yes, there are fundamental differences. One is, if I recall correct, that CBIR is not applicable for (H) licenses, so no competency based IR for helicopters. From CH, I know CBIR only for PPL(A) and CPL(A) but not ATPL, others - see above, call your CAA.