What I think you're trying to say is that runs in certain parts of the deck are affected by runs in other parts. Sure, but that's irrelevant because we're after the average number of runs here.
Think of it like this. Consider the following two procedures.
(1) Shuffle the deck 10000 times and each time count the number of runs. Then average these 10000 numbers; this will give you a good approximation to the answer you want.
(2) Now, this is the same as instead doing the following. Shuffle the deck 10000 times and each time record the following 51 numbers: the first number is either 0 or 1 depending on whether cards 1 and 2 are the same or different; the second number is 0 or 1 depending on whether cards 2 and 3 are the same or different; etc. So for example, for a deck starting RRBRB... we record 0,1,1,1,... Now take the average of the first numbers in these 0-1 sequences, take the average of the second numbers, etc. These results represent good approximations to the (E[X_i]) of the above solution. Add them up, and then add 1, and you get exactly the same thing you got from procedure (1).
This should clarify why it works, and why indicator random variables are so ubiquitous in the solutions of these expectation questions.