Setting up baseline schedule should be in accordance with the contract agreement. The critical path should be the series of activities which is driving the completion milestone date identified in the contract. Whatever manipulation you do as long as it in line with client requirement then it is correct.
But always remember, a baseline is a base line. If you manipulate the relationships of the baseline, it's already called a revised/updated schedule. The baseline critical path will always be the correct one (assuming that the baseline is an approved one) since this is the agreed schedule. If you're having a new critical path based from your new manipulations on the relationships, then the new critical path is your updated critical path and it will only be considered as "correct" once the client has approved your revised schedule. The bottom line is both are correct critical paths as long as the client agrees or approves it/them.
it's always important to understand that a baseline schedule is supposed to be a "reasonable" plan for prosecuting the work. Based on my experience with commercial construction, a baseline critical path typically runs from grading, to foundations through the structural dry-in, mechanical rough, power on, to finishes and punch list work. Since CPM scheduling is a combination of art and science, it can be "manipulated" to create a manufactured or forced baseline critical path. However, such manipulations usually come to light when the subsequent updates and recalculations of the schedule make the projected critical path become more and more unreasonable looking.
If you make a copy of your schedule and then attach the copy as a baseline then you will be working in the working copy and comparing to the baseline.