never tried planting them deep but I wouldn't be surprised if that would be a problem. IME they are by nature shallow rooted plants. Even those that successfully overwintered had roots either at or just barely under the surface.

You can strip/prune as much foliage as you like & plant them as deep as you want. Adventitious roots will form along the entire length of what was the stem, especially at nodes.

Al

If getting leggy perhaps they either need more natural light or move your grow light closer if still indoors? I have snapdragons pop up everywhere outside because I intentionally let prior year's seed drop or I toss some around myself. It overwinters and I get volunteers. Often comes up in goofy places (usually like right under my short fence to keep dogs out of beds. So I just carefully move (keep as much dirt intact around roots as possible) and watch then and they usually do fine! They are tough little things ;)