I've bought lily bulbs many times on clearance that have sprouted, sometimes considerably. I assume you plan to put them in the ground when it warms up? I'd just plant them at the recommended depth at that time. I have often gotten weak bloom the 1st year, not always. I think it depends on the maturity of the bulb whether you get bloom or not.

Yes, once the ground thaws, I'll plant the lilies in their jiffy pots outside. That is how I usually start my bulbs. I just wasn't sure whether it is alright to bury the bottom of the stem when you plant them outside (if I put them deeper outside then they are in the pots)

You should be fine. More than likely the stem will grow rather weakly this year & can use the extra support.