Oh, I'd say that depends. If you would have 1-2 cm overlap, I think that can be fixed with frame angles at no noticeable detriment. Over that yes, just accept it. I have toe overlap on our tandem with my winter boots and fenders. It's OK. There's one 180° uphill turn on a narrow bike trail that can be an issue, but we get around OK as long as there's no traffic.

I ride an old 52 cm carbon Trek with what looks like a normal STA, except that it lands on the DT well forward of the BB. Probably helps frame damping. I have a long torso for my height, so my saddle is all the way back on a setback post, long stem, and I still have more weight on my hands than I'd like, but it works well anyway. I use clip-ons for big endurance rides. The bike's actually a great fit for me.