I was riding a bike w/ a too-small frame. Over the course of a year or so (~3k miles) I kept moving the seatpost up, the saddle back. Never extended the stem but did flip it to lower the bar, stretch reach that way, and then finally gave up. The stock too-small frame probably also had too-short cranks (the bike was well-enough spec'd for a person of the right size, I guess). I don't know about measurable ill effects but it just wasn't comfortable. A friend who is ~5" shorter than me has it now, loves it.