Well, boondocking can mean a lot of things. There is boondocking on government land, which is dry camping in "dispersed camping areas," in other words, open space that is unorganized as opposed to a set up campground. There is boondocking in Walmart parking lots, rest areas, and the like. But then there's boondocking in populated areas, which some people call "stealth camping." This last one is the only type of boondocking where standing out is going to be a real problem.
To boondock on BLM (Bureau of Land Management) land or LTVA (Long Term Visitor Area on various public lands), it makes no difference what you're driving or what color it is. If you're boondocking in other parking areas, such as store parking lots, highway rest stops, industrial areas that are closed for the night, boat ramps, etc., as long as they are not posted as "No Overnight Parking" it is also not a big deal to be driving a lime green school bus. If overnight parking is NOT allowed, it's probably not going to matter what you're driving because any big vehicle is going to get a door knock from security. This goes for government owned land where it's posted no camping. However...
If your intention is to spend a lot of time in cities, to be honest, you probably don't want a skoolie. It's hard to be stealth in a school bus. Shuttle bus, maybe, but most people who plan on living in a vehicle in a city or traveling primarily from heavily populated area to heavily populated area either have a van, a step van, or a box truck, because these vehicles are basically invisible. And they're pretty much always white.
I'm not saying you can't stealth it up in a skoolie, but it's definitely harder. You need really good blackout material on your windows so your presence is undetectable. You need to not snore, at least not loudly, and you can't bring a bark-y dog along. In some cities, it is legal to sleep in your car, and in others, it very much isn't. I would suggest NOT sleeping in your car in the ones where it's not legal. And of course, not sleeping in your car in cute little neighborhoods in the middle of private homes.
If you're thinking about boondocking on private land, as in the back acre of somebody's farm, just... don't.
So... basically... the color really only matters if you're trying for stealth camping on a consistent basis, and even then, no matter what color you paint it, a retired, privately owned school bus LOOKS like exactly what it is, no matter if it's beige or metallic hot pink. Some places are going to be vigilant and shut you out while others are not. But then, that's true even of mainstream, high cost campgrounds, many of which will not allow those unsightly hippie-filled buses into their family oriented parks. You were bold enough to buy a skoolie - why step back now? Make it your own and paint it any way you want. Just know your options may be a more limited, not by the color but by the very nature of a skoolie.