Is a Muslim Married man allowed to have mutah with a Muslim women while he’s already married? (And if yes, does sayed sistani have a fatwa on this with conditions like it being allowed if there’s a special case of wife and husband being separated, also does he need the permission of his wife, can it be without her knowledge,etc)

I’m only aware this is not allowed for him to do with Christian or Jewish

By default Islamic law, yes he can. However:

1- If his wife stipulated in the marriage contract that he cannot unless she gives him permission, then that is binding and he must seek her permission. Otherwise it would be haram.

2- If doing that leads to the break up of his family and loss of his wife/children, then he must avoid that since he is obligated yo protect his family.