I think if anything the SE range strengthens the brand - it stops PRS being seen as "unaffordable" and perhaps encourages new customers to take that next step up. And they use the SE range to make models available which aren't in the USA range - like the Custom Semi-Hollow and SE One.
It's also very clearly aimed at a different price bracket, with no attempt to blur the edges and confuse the customer (unlike, say, Fender, who no longer make it at all clear in their literature exactly which guitars are made in the USA, Mexico, Korea, China...).
And as for the main USA line, PRS seem to be quite brutal in not letting it sprawl too much. Almost every time there's a new model, something else gets the chop to make way - no more Singlecuts, no more McCarty (at least not in their original form).
The Mira is very much a PRS - just a slightly different PRS which, in fact, goes back to the models which inspired Paul Reed Smith in the first place (even though the Mira is Joe Knaggs' design!).