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.