Needed to chance some tires around and put them on a set of Bontrager RXL wheels. These are alloy with a bit of a V. My son has a bag of used tubes so I grabbed a tube with a short stem and when I tried to inflate it, it was too short for the air chuck to grab it. So I replaced the tube with one with a 60mm stem. Now it looks odd so I stopped at the LBS and there was a brand new bike with the same wheels and Trek used 60mm stems so I guess they're OK. Looking online I see there are 42mm stems.

Other than ascetics, does it matter if they are so long?

Stems that are too long will work; they'll just look funny. Longer stems might also be a bit inconvenient if you use an old-fashioned frame pump, making it harder to pump without putting sideways stress on the valve stem. (With a shorter stem, you can hold the rim to brace the pump head with one hand while the other pumps.)

I'm just surprised that Trek uses such a long stem when short ones, that will work, are available.

Fewer SKU's for puchasing and production to coordinate. "One size fits all" trumps inventory management.

There's no issue with longer valves except that it makes hand pumping a bit harder. IMO it also increases the risk of snapping a valve off when pumping with a direct fit hand pump. I use only shallow valves, and am finding it a bit harder to find 32mm valve tubes, so I keep deep stock.

I have seen tubes with a mid length valve, but this is giving way to an "either short or long" selection.

I found that 42mm valves were fine for Bontrager Race rims.