To be fair, the base language of PLT never claimed to support any relevant standard. Instead implementations of standards are built as libraries on top of the base language. So PLT does provide both R5RS and R6RS, both with mutable pairs.
It is when you want to use PLT-specific non-RnRS libraries from RnRS code, you run into pair incompatibilities.
But before this change, I believe every PLT Scheme implementation was a superset of standard Scheme. (Which every Scheme implementation is.) Now it's actually incompatible.
It is when you want to use PLT-specific non-RnRS libraries from RnRS code, you run into pair incompatibilities.