To me it seems the trend towards manufacturer specified mask handling is rather recent (last few years or so) and started with the cheaper fabs. It might be that they want to have the freedom to send an order to any of their partner facilities that currently has free capacity. The old standard where the designer specified the clearance meant that they would have needed to publish their worst specs to be able to do that. Now you the designer never see the specs and just hope that you get what you want.
I personally continue to send fully specified gerbers including mask setup as i want it (to the manufacturers specs of course). And at least the fab i use never gave back feedback that this would be unexpected to them (but they are a rather small fab in europe, so maybe they are outdated with their workflow).
Also consider that if you do not set the clearance and min width in the design tool how would you know that there is enough space between pads to get mask in there. (How often were you surprised that the gerber mask differs from what pcbnew shows. Now imagine the same happens with the 0 clearance specified workflow. But now instead of you being surprised when looking at the gerbers you have this realization when you get your order delivered.)
To be honest i am not really a fan of the warning that got introduced here (and i seem to remember i gave feedback regarding this quite some time ago). I fear this was an overreaction from the dev team about a trend set by certain fabs.