@kookK, great question.
Most of the time it's been in design build, where I work for the contractor. If I was working for the owner, I would inform the owner and let the owner make an educated decision. I would tell the owner that they paid for it and I recommend it, but if you want to ease up on the contractor and aren't worried about it, that's fine.
With that said, I only do this with what I deem to be serviceability issues. In those events, when I am working for the contractor it's his or her call. For example, I could argue it's best practice to design a floor for L/480 live load deflection to keep them from being bouncy, but the contractor may not care. It's not a code requirement, it's not a life safety requirement. The contractor can tell me he wants the code minimum and it's totally ok. It may not perform as well as the L/480 floor, but that's their call to make. Same with slab-on-grade control joints. I show a location that works. If they want to change it up, by all means, go for it. Ultimately, the contractor can decide on some of those things if I'm working for them. And, in reality, the owner is part of that decision, albeit passively. If you hire a contractor for design build, you do it assuming you want the bare minimum, except where you specify elsewhere. Contractors aren't in the business of giving things away, and owners know that. So if they want it designed based on best practices, they probably aren't going the design build route.
Just my two cents. I'd love to hear your response and how you deal with these issues.