I think Axel's mod is more at play here than InitialCrystals & InitialOre not working, because I know the latter two work just fine
As others have (in a roundabout manner) said in the topic, you need to put them under Levels \ GameLevels \ LevelXX , right next to things like GenerateSpiders, PTLFile, OListFile, EmergeTimeOut, RecallObjects. XX represents the number of the level (occasionally some maps don't use this format, but you probably won't encounter them, and in any case the process is the same - put InitialCrystals and InitialOre next to those lines)
I'm not sure how Axel's Mod works - or more accurately, how your installation is set up :S If there are still .WAD files around, then LRR won't read from the Data folder unless it has to, and will read from the WADs instead: so you'll want to unpack the WADs, make your edits to Lego.cfg there (don't forget to save!), and recompile the WADs.
As for unpacking and recompiling your WADs, Wad Recycler is by far the best tool for the job:
https://www.rockraidersunited.com/topic/3742-wad-recycler-2/
and is pretty straightforward to use (drag WAD into window to decompile, drag folder into window to recompile
Posting a screenshot of what your LRR installation looks like could help, as I'm not familiar with Axel's Mod.