Probably there is also some waste when people use free Janelia dyes on projects that might not have seemed worthwhile at $138 per 300 μg.

Because basic research isn't nickle-and-dimed enough already, let's consider pre-emptive waste.

Here's the thing: it's not about the material cost. It isn't. The synthesis for most dyes is piss easy and can be handled by most undergrads, but unless you train them hands-on and tell about all the weird quirks that can't be packed even into supplementary materials for your paper, it's gonna have a pathetic yield. Story time!

During probably organic synthesis 2 lab, I achieved a higher percentage yield at higher purity than even our lab techs. See, the reflux column had to be open-topped to avoid containing ether vapors. I'm fuzzy on the details but whatever we were making was super-sensitive to water, the humidity in the lab was off the charts, and ether has the tendency to pull the water down the column.

I looked around, asked lab tech for a glass airlock tube (that S-shaped pipe, same you'd use for alcohol fermentation) who was reluctant to give it to me until I told what for. I took some anhydrous magnesium sulfate (very hygroscopic), ground it into fine powder, put it inside the pipe. Nope, it wouldn't work, efficient enough. So I dripped a bunch of dry acetone there, and moved the slurry around to cover all the walls of the pipe, then blasted solvent away with a heat gun.

My yield was 91%, the second highest was 23%. Lab tech said he never got it above 86%.

I can easily imagine the know-how for those bespoke dyes being about four orders of magnitude more complex than my shitty little McGuyvering. You probably need to take tiny bullshit elements like the thickness of the glass into account, because if step 4b cools too quickly your reagent crashes out and simultaneously stops further reaction while being a slurry mess of a headache to separate from your dye. Some simple some recondite as fuck until someone will do the "monkey see, monkey do" portion of the training.

Sorry for flippant line in the OP, but if you gonna hinge your further reasoning on arguments like "wasteful scientists"... dude, seriously?