Easy answer first - consult the installer about applying products prior to install. Depending on the film being used and the shop they may have varying instructions on what to do. I've heard of some shops recommending nothing be applied, others tell you to use your preferred product, and some don't care either way.
As for the color difference, the only time I've experienced color variation between a clear bra covered area and non covered area was a case where the owner hadn't cared for the paint that well (and it was red) the fade on the paint was obvious, while the area under the bra was still fairly fresh looking.
So IMO, as long as you do a good job of keeping a nice coat of protection on there (wax or sealant) it shouldn't be a concern.
As a side not make sure to tape off the edge of the bra prior to any polishing or waxing. Product likes to cake up along that edge and make it visible. just running a bead of masking tape (blue or green 3M) will keep it protected and prevent that problem.
Hope that helps.
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