Some technologies prohibit "circuit under pad" and some promote it.
You'd have to get specific and look at your PDK's I/O construction rules.
Underlying topography should not bother the assembly process but
assembly "inputs" (like wedge bonding) can put strain on active devices
which either is, or looks like reliability degradation. A fabrication process
that allows "CUP" (circuit under pad) has to be qualified in concert with
a specific assembly recipe and vendor's control system.