As far as I'm concerned under block exemption you can have the car done/repaired under a warranty at any VAT registered garage providing that:
1/ The repair is carried out using BMW supplied parts. Customer should/must for their own protection and validation retain if presented/made available any documented receipts for any parts used should in the future the repair called into question.
2/ The repair is carried out in accordance to the said manufacturers/warranty company's code of practice(how do you prove/disprove that this has/hasn't been done as they'd wish/require the repair to be carried out)
3/Everything and the decision as to where the car is repaired should as far as I'm concerned should from the end user be fully stated in the claim o the warranty company under their claim procedure process before any repairs are carried out.
We've done a good few warranty claims and haven't come across any issues the key is keeping the warranty company informed and from the repairers side not over egging the claim.
Re the difference in warranty prices between main dealer and indy tough one really as I suspect the labour difference would deter some dealers from perhaps taking the work on as on a budget which hey have to meet it may not be viable.