Clomid antagonizes the androgen receptors in the area of the nipple, among other things. This blocks the agonization of those receptors by estrogen. If you are taking any aromatizing AAS (i.e. Test, D-bol,etc.) then you will have elevated levels of E. Clomid doesnt DO anything in the nipple, it just keeps E from doing anything, like giving you little titties like i had when i was about 10 yo.
Clomid also agonizes the pituitary gland to encourage it to produce LH. LH stimulates the gonads (testes in you, ovaries in me) to make T. So Clomid probably helps to get your HPTA system working normally again after the cycle.
No reason not to take it all the way through the cycle. Men have stayed on 50mg ED for a year or more without any problems.