Any form of regulation is attacked by those who seek to profit by freely causing the harm that regulation prevents. These attacks aim at completely eliminating any and all regulation, but also aim at eroding it so that complying with the letter of the law is ineffective at actually complying with the spirit of the law.
Trying to make mountains out of molehills is one way to attack regulation.
Look at OP's example. In no way did OP offer any support for the $100k price tag for certification, or even mentioned what this hypothetical amount represents in the total investment in a product such as an engine. We're talking about investments that range well in the tens of million of dollars. It's an insignificant drop in the bucket. The design team's salaries alone eclipse that value. On top of that, a single engine alone sells for thousands. Is this hypothetical regulatory cost that high if it can be covered by selling a few dozen units?
The combinatorial explosion is also a far-fetched example of this desire to make mountains out of molehills. You do not need to recertify a whole engine if you do a minor change out of a whim such as changing the color of a knob.
Ultimately, the goal is to ensure that whoever wants to sell an engine isn't putting out subpar products that underperform and outpollute at clearly unacceptable levels. If proving that your product is not poorly designed and irredeemably broken is too much to ask, is regulation really the problem?