I believe there are issues but that a fairly accurate magnetic survey can be obtained by taking fore and back sights and by staying in the middle of the passage (e.g. not near the walls). Ed W will tell you exactly how accurate the surveying can be as he has done quite accurate magnetic surveys in Iceland.
Multi entrance tubes or braided tubes will give opportunities to check the accuracy by a surface survey between entrances or around loops to check misclosure
I would guess that for real critical surveys then a theodolite survey is your best bet.