Keeping modifications to key source files to a minimum has always been one of my objectives. However, phpBB is somewhat limited in features. It really is "what you see is what you get"... and nothing extra. This means that even very small and trivial features require workarounds and mods.
As the development gets closer and closer to completion and features are constantly added to get the best overall package... the list of mods increases accordingly. At this time it's quite a list. To give you some idea. This is the 90% finished ModX for the upcoming Beta 4.