I'm sure nothing would go wrong, but just to double check. I plan on using Brett B. for a 3 gallon batch in a 5 gallon glass carboy. That shouldn't be TOO much head space correct?
I have the same thing going for a BDSA, except I pitched Brett L. I'm a firm believer in the protection of the pellice. If you were really worried about it, you could flush with CO2 before transfer.
Don't have the equipment to flush. The primary ale yeast should finish around 1.022 so the brett should be able to produce enough CO2 to protect right?
Brett will take a long time to really get going. Add a few ounces of table sugar (dissolved in boiling water) to the wort when you transfer. That should generate plenty of CO2 to push out the O2 that's in the air. Once that's cleared out, the headspace should be of no concern.