When I drill a hole before inserting an anchor bolt: You say "I drilled a hole."

When I drill a hole before pulling a wire through it: You say "I drilled a hole."

When I drill a starter hole before using my jig saw: You say "I drilled a starter hole."

And, based upon your post, you knew that all along!

"...the most common interpretation of pre-drill is, in fact, to drill before driving a screw or nail..."

Context controls. The OP was, in fact, referring to drilling pilot holes - no need for "interpretation" at all.

A language has constructs, rules, if you will. Ostensibly, we were all taught such things as part of our education. To argue a point one needs reference to the rule as opposed to anecdote and references to one's subjective apprehension of what is 'common.'

"BTW...Is it pre-drill or predrill?"

According to Miriam Webster online, the later is preferred and the former will serve. Since neither makes any sense, why worry about the rule for hyphenation?