I recently purchased a spartan 9mm side charging upper receiver with LRBHO and a Spikes tactical 9mm lower receiver with LRBHO (Glock version) both from Joebobs.

I've heard that LRBHO on the 9mm lowers is much more reliable than the uppers.  Can anyone confirm this?

If so...

I would like to keep the LRBHO on the spikes tactical lower, but the bolt catch housing on the lower receiver is making contact with the inside of the side wall of the upper receiver by roughly .75mm.  It shouldn't be a problem to chisel it out, but I figured I would ask here for any advice on the situation before proceeding.

I don't have any experience with a LRBHO lower.  As far as the LRBHO upper goes, I've had one for three years and after an initial extremely slight adjustment bend to the actuator rod angle, the LRBHO has worked 100% on three different lowers - one dedicated Glock 9mm mag type and two standard magwell type using a non-LRBHO Glock 9mm mag magwell adapter.  Note, I did have to file out part of the right side inner lip of the LRBHO (billet, non-mil spec) upper for clearance to the top bar on the non-LRBHO Glock 9mm mag magwell adapter.
Best of luck with whatever you pursue.
MHO, YMMV, etc. Be powerful; be well.

I've had a QC 10 glock lower for 5 years now......absolutely love this thing...........that said........the LRBHO on it sucks..........Rube Goldberg affair..........I bet I spent the better part of the first two years screwing around with it..........finally I removed all the parts and bagged them........I just didnt have any luck with it at all............

 Buy a non-LRBHO side charger upper

Then sell, or keep the LRBHO side charger upper.

Problem solved.

My Colt gun has it on the lower, Spikes. Never any problems.
My Glock mag gun has it on the upper, New Frontier. Never had any problems.