I am presently enjoying the GOG release of Doom and I do have a question--The two apps seem to share the same save file path, so would playing a map that replaces Level 1 on the Master Levels, saving the game, quitting the Master levels, loading Doom II and loading the save file have any consequential effect?

DOOM will bomb out with an error in this case. Just like on any other attempt to load incompatible with the map saved game. It would be wise to either have separate copy of DOOM II installation just for the Master Levels; or have a batch-file, which will backup and restore saved games automatically.