That's the key, pristines aren't special unless you want something forever, an ignoble bee still lives about 150 generations on average, never less than 95. Even at Shortest that's a minimum of over seven hours, and 950 production checks, at Longest it's an average lifespan of about 81 hours and 10.6k production checks. Ignobles really don't die all that fast.
I used to ignore Ignoble bees completely, and I'd rage at how low the percentage of Pristines are, in the wild. It meant I'd throw away 8 of every 10 Princesses because I wouldn't use the Ignobles.
But then I realized Xavion is correct - there's no reason not to use Ignobles for everything, and then simply switch to a Pristine once you've achieved what I call a "Production Bee", which is intended to sit inside an Alveary and crank out its specialty product forever. Only at that point do you require Pristines, and you can very easily do everything using Ignobles and only create a Pristine as the final step in the process.
I've always done much of my bee-work manually, however in my last play-thru I did use Gendustry for the first time... one of the problems with Gendustry is that the mod's machines do kill off Ignobles at a higher rate than Pristines, so it can be very frustrating to lose so many bees along the way... but that's what made me realize I absolutely had to use Ignobles even tho Gendustry kills them off occasionally, because at the rate they die, I needed quantity of bees, not quality...
But if you're doing "vanilla" bees, without Gendustry machines, then the rate of Ignobles dying is so low that there's no reason to avoid them.