I believe Simon is on the right track, but I see that the patches completely remove the "Conflicts" relationship. Given that the following package do have file conflicts, I think that change is incomplete:
https://packages.debian.org/bookworm/all/golang-github-golang-protobuf-1-3-dev/filelisthttps://packages.debian.org/trixie/all/golang-github-golang-protobuf-1-5-dev/filelistI am thinking that the "Conflicts" relationship needs to remain, but needs to be accompanied with a mutual "Breaks" relationship. Additionally, I suggest modifying the golang-github-golang-protobuf-1-5-dev package to declare a "Replaces" relationship against the package golang-github-golang-protobuf-1-3-dev. The thinking here is to help apt to prefer packages that do work with protobuf 1.5 in favor of those that don't.
In general, Matthias is correct and protobuf 1.3 and 1.5 are known to cause runtime crashes. As such, packages that still require 1.3 need to be updated or removed from testing.