At the risk of sounding like a stuck record, there are many, many factors which may influence how much vaccinations cost at each practice and it's got nothing to do with them being cheeky. In fact one factor I haven't already listed above is that the wholesalers charge different prices, so if a vet is tied to a particular wholesaler, they may be stuck with a higher vial price. As Jane said, any veterinary relationship is built on trust - so if that trust isn't there or you feel the quality of the appointment isn't good enough, by all means go elsewhere...but thinking that a vet is being cheeky for charging more for vaccines, when they might be covering their overheads in another way, or doing something like heaven forbid paying their nursing staff a decent salary, is not indicative of that trusting relationship. Of course anyone can do what they like as long as the vets are accepting of that, but IMO it risks both the quality and consistency of clinical notes (even knowing in an emergency that things were normal on x date at a previous vaccination elsewhere might be vital - and be honest, how many people do transfer all the clinical notes backwards and forwards straight after seeing a different practice) and trusting relationship which is of such importance when there are critical decisions to be made.
It won't be cheaper to do that - most of the cost of the vaccine is the vet's time and other overheads, not the cost of the actual vial of vaccine itself. And it generates additional risks of proper temperature control of the vial so it might not work at all by the time you get it to the vets...most of the vaccine failures I've heard of with RHD2 have been from self-administered multi-dose vials, and while I can't substantiate this, I suspect inadequate temperature control is the main culprit. But yes, definitely ask about multi-rabbit discounts...nothing ventured, nothing gained!
The more I read this thread the more I realise that my vet would be considered expensive...I spent a lot of time there though and I know that they aren't taking the mick. In fact their accounts for last year show that they turned a net profit of £7k. £7k for all that hard work and stress over an entire year.