I believe Arduino software, owing its save system, shuts "indexing" off.
I don't think so. At least, I've been running Arduino since about v0015 and haven't noticed spotlight turning off.
(OTOH, I'm still running Mavericks.) I'm not sure what you mean by "owing its save system", and can't think of a reason that Arduino would want to turn off indexing. (and, just checked, spotlight finds recent changes to a .ino file just fine...)
I also had the same issue a few weeks ago, I just deleted the index file and started reindexing. After this procedure Spotlight worked normally. Spotlight had this issue only when I switched to El Capitan. I also believe it could be the Arduino Software.