+1 on speaking with the engineer.
In my mechanical engineer days these issues would come up regularly during wiring/HVAC etc. A quick sketch and/or phone call was always appreciated and we could work something out on how to go about it, generally in under 5 minutes.
There are so many neat, quick ways in the electrical world to attach conduit to structural steel. Many don't even require drilling. B-Line & Cooper have some wonderful stuff.
If I came on the job site and found some clown had borrowed the mag base drill and put two dozen 1-1/2" holes through my structure I'd blow my top. I had enough trouble with the fabricators doing it... They'd be proud of themselves for saving a half hour of shop rate time, completely unaware that they'd invalidated a structural calculation requiring 4 hours of engineering time to redo, recheck, restamp and reissue. While I had to go to the client with hat in hand to get it okayed and explain why we can't control our configuration.
Of course, this may be existing structure with no engineer in charge. To give you his opinion he'll want paid. Either way B-line is looking good