I got a whirlpool bath tub and I am putting tile above it. I drilled into the top of the tub and then nailed it in with roofing nails. Then I read the directions and see that the nails should be above the flange that I drilled and nailed. They advise against drilling into the flange and mounting it. What is the problem with drilling and nailing the tub flange to the wall studs?
Typically you pin a nail/screw so that it rests on the top of the flange holding in place by friction more or less not nailing through the flange. I would do like your supposed to do and calk those holes you made. The reason is most likely to get the fastener further away from water, not making a hole, and not risking the tub settling or cracking from you puting a hole in it.
Ultimatetouch Kitchen Remodeling Chicago, Bathroom Remodeling by an Illinois Remodeling Company