I have manually deleted files from a built game and I found out two things:
1. FPSC is finicky about what you can removeIf you manually remove files make sure you make a backup copy of the files first.Bad,bad things can happen if you don't.
2. While removing things like enitites may decrease the filesize slightly and can affect the speed of gameplay the effect that it has on the size of the files has been minimal.And FPSC is weird.In some cases it will only put the things you use in some places while placing every file in a folder in others whether it is used or not.
The way FPSC is at the moment means file sizes are going to be pretty big.While packing or compressing the game may help in storage or movement of a game it might not make much of a difference when the game is unpacked/uncompressed.
I use FPS Pack and while I do notice a considerable change in the size of games at times at others I notice little to none.
When TGC releases an update for FPSC I hope they address the issue of large filesizes as I am sure we all do.