There is no requirement in any IRS pub I can find, that says you are required to use the same method for all splits. For rentals, IRS Pub 527 applies and that pub does cover aspects of renting out a part of your home.
When it comes to depreciation, whatever method you start with, you stay with. You can't change it later.
When it comes to utility deductions, you can actually change methods each year.
One thing that I do need to point out, is concerning a landline telephone. The IRS states that if you only have one telephone line, then you may not allocate any of that costs to the SCH E. It further states that if you have a 2nd phone line and that 2nd phone line is for the exclusive use of the renter, then you can claim 100% of the cost of that 2nd line on the SCH E.
For all other utilities, they must actually be shared with the tenant in order for your to claim a pro-rated amount on SCH E. If it's not shared with the tenant, then you can't claim anything for it on SCH E.
