tl;dr: Despite what Dr. Pym says (more than once), Scott didn't have to slip "between the molecules" of titanium to get into the suit; however, he had to disable the size regulator, and that meant he would eventually get sub-molecular, because he couldn't stop himself.
The movie makes liberal use of the term "sub-molecular" but it clearly doesn't understand what that term means. The problem with taking the movie's dialogue at face value is that it is directly contradicted by everything we see on screen:
- He doesn't actually slip "between the molecules" of titanium; he slips through a seam between two distinct titanium plates on the suit.
- Once inside, he's shown to be larger than electronic components like ICs, which are usually bigger than the insects he's been running around with, let alone single molecules
- As he keeps shrinking, we see him go past other microscopic items, like bacteria and whatnot, that are clearly larger than molecules.
- Eventually, he shrinks down to the point where he's seeing DNA molecules -- but those are big molecules, and he's bigger than they are.
It takes until very near the end of that scene until his size could legitimately be described as "sub-molecular".
The most generous interpretation I can come up with is that, even though Hank Pym literally said "slip between the molecules", that he wasn't speaking with scientific accuracy, but was dumbing things down for Scott's benefit; what he meant was "become much smaller than normal, and eventually sub-molecular, to fit into that gap." It's very, very thin, but as far as I can tell, it's the only in-universe way to explain the scientific disaster around the whole concept.