I never really worried too much about the physics of the shrinking process since I never saw Shrinking Man as a hard-science piece. It's like wondering where the Hulk gets his extra mass from or how the Invisible Man can see. The story is about the "what if? premise; the technobabble is just hand-waving to justify the central conceit. Or so I always saw it.
Ultimately, from what I understand of biology and physics
, if someone were to nitpick the entire concept it quickly falls apart regardless
of this point. As you say, the idea was to establish a "what if" scenario and then jump off from that. If Matheson had tried to be "realistic," the story simply wouldn't exist.