an OTR may well upset things... but as has been said NUMEROUS times, if you modify the way the engine works with any performance parts, it will need to be retuned. Retuning your car will not screw up it's reliability if it's done properly. From what has been explained to me by the guy at G-Force Performance, if you aren't putting a cam in, you can get a sweeter tune with the MAF in place. I have a pod type CAI on my SS with extractors and 2 1/2" Hurricane system..... stock SS on the dyno usually do about 270rwhp, mine retuned now has 330rwhp, which i think equates to 247rwkw. That is 300+ engine kw. My car will now easily spin the rears off the mark (auto) and will easily drift on corners at 140kph in 3rd. It got check engine codes prior to the tune due to the new exhaust, but none since the tune.
You can have an OTR and maintain the MAF if you wish, a lot of them are made that way.
From what i have been told, and that was from a guy who used to work for Holden who now works at the mechanic where i now take my car for services due to the Holden Dealer charging an arm and a leg, the Holden dealer can overwrite any retune if you don't tell them not to. Usually a MAF tune is cheaper than a MAFLESS due to the cost of the access codes or whatever it is the tuner needs to get into your ECU.