I haven't tried RTR but in RTW 1.1 I was playing as the seluclids and getting hammered by egypt when they demanded I became a protectorate. As I had nothing to lose I accepted to see what'd happen and it was not a whole lot. I played trough the whole campaign and didn't notice much difference asides from Egypt stayed an ally right through. Even when they were down to two or three provinces and I was charging on towards the 50.
It's never happened since so not sure these days.
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