I think either way potentially could work. I've tried combining double front squats with clean and presses in various ways, and there's no one right way as much as it's just about finding the balance between the SQ volume/effort, C&P volume/effort, and overall session effort that feels good and right for you.
Just from mentioning rerunning 3.0, I'm guessing you liked that format, and feel like you could still get more out of it, so I'd lean toward that. I think the rep scheme definitely lends itself more to going rep for rep with presses and squats.
In my experience, once the reps start getting above 4 with a relatively challenging weight, a complex of C&P and FSQ gets to be a little too much. Each set just gets to be a little too much of a fight and requires a little too much recovery to get a good volume, and it just doesn't feel as good anymore. It shifts from being an autoregulated strength program toward being a tough complex program, where I feel like I should really drop down a bell size, or just switch to one of Geoff's programs of complexes.
I just did a five or six week experiment with C&P/FSQ complexes building up from sets of 2 to sets of 5. The weeks with sets of 2 and sets of 3 went really well, but I felt like I was running out of gas once I got to the first week of sets of 4, and I abandoned it in the middle of the second week of sets of 4 (I was doing the same number of reps per set in each session for the week, but varying the number of sets each day).
Alongside Giant 1.0, I've had a much better experience separating the squats and doing something like 2x5, 3x5, or 3, 5, 7 before or after the C&P sessions. Your option A of limiting the number of squats might work, but I'd consider inverting the number of squats and presses. In other words, 3 squats on low rep press day, 2 squats on medium rep press day, and 1 squat on high rep press day.