Yes, this is fully intended to prevent you from releasing screwed up mods. The internal MAPINFOs contain stuff that's subject to change without notice which would break your mod.
The problem with wholesale replacements like what you did is that if there is one little addition -- like externalizing another hardcoded thing into the gameinfo block for example -- then the whole game crashes down. Because before that piece of data was in the exe, now it's expected to be in the pk3, and unless you update your override mod it will not be. The game tries to access it, finds nothing, and aborts or crash.
You can still do you mapinfo replacement thing. Just make a different file for each iwad and use the ini's autoload feature to load them as appropriate. This way, the core mapinfo files are still read entirely and additions do not provoke crashes.
Another example, when the generic damage factor feature was introduced, the updated actor definition for Actor was at first forgotten by mistake. As a result, the game didn't crash, no, but it defaulted to a default value of 0, meaning that nearly all actors were now immune to practically everything since they had a damage factor 0.
So you can expect only problems from doing things this way. You should not try to be "clever", especially not when there are already perfectly working methods to do what you want to achieve.