You’re probably OK with ignoring those errors, but setting it to 3 mil is a good idea.
The issue that it’s warning you of is mask registration errors. When the fab puts the mask on there, it can potentially be slightly off, so the whole mask layer is shifted relative to the pads. This picture is a good example of this. The 3 mil mask clearance ensures that if there’s a shift, then it doesn’t cover up the pads (or at least minimizes the damage). It’s also possible for the mask features (eg, the hole over the pad) to be shrunk or enlarged slightly, but typically this is covered by the same spec.
However, this is NOT a case where bigger is always better, since excessive mask clearance can pose issues as well. As an example: If you have a board with 6 mil trace spacing, a 5 mil mask clearance, and a 3 mil mask shift, you get something like this:
As it looks in the design tool
Worst-case scenario from the fab
In this case, the fab is within spec, but still manages to expose the ground plane right next to your pad. Still usable, but it’s a bad situation that will lead to shorts if you’re not incredibly careful. This is mostly an issue if you’re not careful about mask as you decrease isolation, but it’s a really nasty trap.