Let me explain by going over why its problematic in the specific case of the iMac (which also handily explains why its a problem in other Macs.)
The main issue here (IMHO) is transparency. Just looking at the spec sheet on Apple's homepage one could reasonably assume the only difference, aside from storage capacity between the two 24" iMac options is 1 GPU core (or about a ~9% performance deficit in heavily GPU bound tasks based on previous M1 macs). This will undoubtedly lead some people to conclude they don't need that extra 9% GPU performance (maybe their workload is CPU bound) and just order the stock config, or CTO a 7C GPU iMac and used the money saved to go for 16GB of ram (for example.) Many of those people could be in for a rude awakening when they realize they've actually bought a mac with a significantly worse cooling system and consequentially slower performance/more noise.
To be clear, I don't own a 24" M1 iMac, and given how the M1 performs in the MBA/MBP/Mac Mini I don't expect cooling to be a major bottleneck, but it's still a major difference between the models that Apple needs to be clear about if they're going to use this as a point of differentiation going forward. While it may not matter much today, next year (or even later this year) when we have an M1X/M2/M2X/etc with more CPU and GPU cores and a potentially higher TDP, the differences could be quite significant.
So, to recap, the differentiation itself isn't the problem, the issue is the completely non transparent way that Apple is going about it. With Intel Macs, you generally knew what kind of performance you were getting by looking at the CPU/GPU on the box/spec sheet, and could thus make an informed decision. While there were a few Intel Macs where Apple really messed up the cooling, this tended to be the exception and not the rule, and typically applied to all SKUs across the product. Also, Apple doesn't get a pass on this kind of behavior just because they increased performance X% over last gen.