I am a huge fan of the Boring but Big template for this exact reason. I have improved my numbers significantly in 4 cycles and I think a lot of it has to do with getting lots of reps in the 4 main lifts.
I still don't get the "direct" argument. By the same token, the only "direct exercise in that program is the leg curl. Squat's aren't "direct" leg work, rows aren't "direct" back work, Bench isn't "direct" chest work, pressing isn't "direct" shoulder work.
Big thing in these forums is "OMG direct arm work for big arms, if you donâ??t do curls you are going to be stuck at 10" arms!!!"
I personally think the whole thing is pretty stupid. There is no such thing as a "direct" or "indirect" exercise. Just because an exercise involves multiple muscles, doesn't mean it isn't directly working them. They are contracting under a load. Period.
Now it is true that people will natural emphasize one muscle over another in an exercise, but that can go either way for any muscle and can be controlled by concentration if you really get down to it.
Like, I said, squats aren't direct leg or quad work, but no one seems to barge into threads claiming you cannot get big quads without doing "direct" quad work.
Based on the individuals leverages, technique, est. some things work and some don't. Arms are no different. Find things that work what you want worked and ditch the stuff that doesn't. There is no real difference between a "direct" and "indirect" exercise, and there is definitely no rule saying you can't succeed without choosing at least some exercises from some made up category.
And the conditioning side of 5/3/1 should probably hit calves pretty hard.