Do you think Joel would not attribute a significant amount of the financial returns his companies have seen to his cultural choices about providing the best workplaces, even when it cost him a lot to do so?
Of course, since you can treat programmers as adults, you can just explain that to them. And, with whatever funds and free variables that you can work with, you can focus on providing the healthiest workplace available at your budget.
I don't see a lot of companies running into this issue though. If you're at the point of receiving VC funding, then you can afford to give everyone an office. 4x rent + $500k up front is round off error for a lot of firms, and even for some firms where that would be feasible-but-expensive, it's probably worth it.
What I don't see, though, is a bunch of firms actually running the numbers here. No one is pragmatically checking whether they can give their employees this thing that would be super great for the employees and for the company. Instead, I see a lot of people looking for excuses, a priori, to not invest in it, and to instead put the money towards over-the-top, opulent expenses, and designing a workplace that functions more like peacock feathers than as a workplace.
I would totally agree with you if I looked around and saw a bunch of VC firms or founders going "shit, I'd really like to make a healthy and productive workplace for my employees, but the budget is just too tight." But I don't see that. I see people who a priori place more value on the status aspects of workplaces than the functional or humanity-affirming aspects, and as a result want to confirmation-bias their way into rationalizing decisions to make every wall a transparent soap marker surface cuz it looked cool in A Beautiful Mind.
Higher rent + long, time and attention consuming build outs + accounting nightmares are more expensive than you think.
Look at Joel Spolsky's story. 4x rent plus $500k in extra buildout. http://www.joelonsoftware.com/items/2008/12/29.html