No company does this. Prices are set based upon demand. This does provide opportunities to make more money during some periods than others. If you have a monopoly then you can ignore this and just pick what makes you the most.
> Apple seems to think charging $99 a year for developers will help its long term bottom line the most.
It's absolutely a bespoke filter to prevent spam and automated misbehavior. Admittedly there does seem to be a resulting overall quality difference between iOS apps and other platforms.
> Prices aren't justified or not, you choose to pay them or not.
Business models are legal or not. You choose to play by the rules or you don't play.