The more I think about this the more (I think) I see an interesting trend emerge. I'll limit this to the past 10 years or so as to not conflate the issue with the quarterbacks in the option offenses of yesteryear..
When it comes to the true mobile/dual threat college QB's, there have been truly elite ones - Mike Vick, Lamar Jackson, Vince Young, Tim Tebow, Pat White, etc. Virtually all of these guys are blue chip recruits due to their elite "can't miss" athleticism. Whereas, some pocket passing QBs may not have been as highly recruited, but became elite QB's (see Drew Brees, Tom Brady, Aaron Rodgers) and many, many others became very good QB's.
If you are not one of the elite schools, you probably can't count on getting the next Vince Young. But you can try to find the next Drew Brees. I don't think it is coincidental that we've not had much luck with mobile QB's. I think the trend shows that unless you can recruit one of the elite athletes of the class, you are better off recruiting mid level pocket QBs than mid level dual threat QBs.
So yes, if one of these elite mobile QBs fall into your lap you customize your offense for them, which I think Brohm would do. But not some guy who runs a 4.7 40 who is considered dual threat because he can run by high school linebackers.