Amber glass is said to be best to block sunlight, colbalt next. But glass color is not as important if you store your joose in a cool and dark place. I mostly use 120ml, 240ml and liter amber glass, some colbalt glass I also have some that are clear glass for cold storage in the refrigerator or the freezer, and 30ml luer lock bottles on my desk for filling the Reo bottles with. Glass has been the Old Skol preferred for long term storage, but there are some plastic bottles now that work just as well except for with a few known flavor extracts that can degrade plastics. I also store my base in 1 liter amber plastic bottles in the freezer (and still have some nic in amber glass as well in the freezer even though I don't use it in my DIY anymore).
So IMO basically what Papa Laz said other then there is no need to have the caps off the bottles when they are in the UC (where they can tip over sometimes). Water level is the key for the tippers, but it doesn't have to be as high or higher than the joose inside to properly age the joose either. My UC has a 30 minute cycle that is perfect with room temperature water, does not over heat/cook the joose while warming the water enough to age faster. So I never turn on it's heater for aging joose. If you "breathe" the joose to bled off any chemical tastes that is needed with some flavors, you can do so caps off in a dark place after the full UC treatment when you are letting the bottle(s) of joose rest for up to 24 hours to finish being fully aged. Many flavors do not need to be breathed at all. Also, I prefer to call it aging the joose because you are not steeping to extract flavor, rather you are thoroughly mixing, evenly distributing and incorporating the flavors and your base all together.