It might be a specification issue. I have been on jobs that seemed to say "Do not install conduit on top of the bottom bars." But I have no idea why. On other jobs, anything goes. However, if you are running conduit parallel to the joist, it is wise to run them along side instead of on the bottom. The reason being that sometime later, someone may have to run another conduit perpendicular to the bar joists along the bottom and the bottom should be clear for this. Also it is inadvisable to run conduit above the joists in the roof corrugation since it would be vulnerable to damage by the roofer's long screws. ~Peter
It does seem to vary by job, but if it's a hassle you can generally get the requirement to stay off of the lower bar waived. Just ask the owner if he wants you to testify as part of the lawsuit - the lawsuit against the structural engineer who designed a roof so flimsy it couldn't stand the additional load of a conduit, much less a replacement roof.
It's amazing how much stronger those joists get when you do that.
Few years ago, I was running some 3/4 homerun conduits and the GC told me that I needed to run all of my conduits as close as possible to the weld points of the bar joists. I told him that may be true for hanging transformers, bussduct or other types of heavy equipment, but not for EMT.