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.
The latest standard, R6RS, goes no further than grumbling about mutable pairs and raising the possibility of deprecating them in the future:
http://www.r6rs.org/final/html/r6rs-rationale/r6rs-rationale...