You're right. They are included for coverage testing for both 403(b) and 401(a) plans. Mostly, we don't worry about the effect of this on nonprofits too much though, because the number of people treated as independent contractors is small enough that counting them for coverage purposes (even if all of them were recharacterized) would not throw off coverage testing. There aren't a lot of nonprofits that have Microsoft's situation.
The bigger issue is the universal availability rule. That's a damned if you do and damned if you don't situation. If you include someone who really is an independent contractor, you have violated the rule that a 403(b) plan can cover only employees. If you fail to include someone later recharacterized as an employee, you have violated the universal availability rule. So there is no "safe" option other than avoiding having independent contractors at all.