The worst that LA could do to a nonprofit fan game project would be ultimately to file legal suite for copyright infringement. Digital copyright laws in the US
include nonprofit infringement.
However, if the files were not publicly distributed (i.e., during development) then a C&D would likely be the most they could get away with. Of course, they can afford a much fancier lawyer (Stan!!

) than I can, so if they really ever wanted to press the issue, they probably would. Not necessarily that they would have a legitimate case, but they could tie it up in so much legal red tape that it would financially ruin me for life.
That is being a bit overly dramatic. If such a project were ever started and LA were to C&D it, development would be stopped instantaneously. I'm not one to try my luck on that front. I may consider trying to negotiate afterward, but development would be stopped until further notice.
As for TTG being more lenient, yes, they allowed this game, but don't forget that they C&D'd the ToMI 2D project. Even TTG has their limits on what they consider acceptable. One-time usage of their characters, referencing their storyline is apparently okay (in this particular instance); continuous usage of their copyrighted materials may not prove to be so.
Just some thoughts. Copyright is a very fickle thing at times, largely depending on arbitrary decisions whether it is acceptable or not. Lots of gray area.