I offer experience, but probably not wisdom.
My son was about 46" tall when he started riding a
Raleigh Rowdy 20, the 2017 model. I think it's more or less the same bike as the Lily. We replaced the stock 60mm stem with a shorter, cheap,
35mm one from Amazon. The original was just too much reach for him. The shorter one, along with the handlebars being adjusted so that the rise was angled back toward him, helped with the fit. The intent is to put the original stem back on as he grows. I haven't noticed any problems with him riding on it with the shorter stem. He joined a local kids mountain bike team in the summer of 2019(it's sort of like a summer camp activity) and enjoyed it. Younger kids like my son were on all kinds of bikes, mostly BMX, and were riding on easy local mountain bike trails. With the Rowdy we bought it used for this year knowing he'd be on those trails, so the aggressive design/fit was a little more appropriate for that kind of riding. I think you could probably get away with a short adjustable stem and not have any issues. The bike may be just a bit more squirrelly than it was before.
My son has complained a few times about soreness from the seat on longer rides, but I assumed it was from the longer rides, not necessarily about the seat. Also, he's scrawny, so he doesn't have much of his own . . . padding.
If it's useful, the image below shows the fit with the shorter stem when he was about 46" tall. We also modified the bike from a 6 to a 7 speed to add a 34 tooth gear, with a new derailleur, and trigger shifter.
