No, but for designers designing with an unknown/potentially changing font is more work and produces less good looking results. So unless there is a set of reliable cross-platform system fonts there is zero incentive for designers to use system fonts for commercial projects.
If you have ever worked in design the absolute horror is if you designed something well and then the boss of the org tou did it for opens it on their IE6 and it looks like shit. This is a similar problem.
Is it truly designed well if you didn't find out the target audience and the tools they would be using to view that design?
I love good design. I really do. And it truly is a critical piece of good software. Yet the most painful experiences I've had in my careers are from working with designers who who push their idealized design philosophies onto a reality where they aren't the right answer. Designers need to be as focused as anyone else on understanding the customers and solving the customer's problems.
I agree with you. There is a lot of bad design and there are a lot of bad designers. Privately I tend to call design that doesn't conaider function styling and people who make these decisions are stylists.
That being said designing for screens is already hard because the sizes and proportions of the screens and windows can vary wildly and even change during use. Adding potentially different fonts with wildly different widths and readability into the mix is certainly something that doesn't make things easier.
Again, that doesn't mean using a system font is something I'd never do, it just means that whether that is a smart or a bad choice depends on all kind of factors.