Apparently repeated meristem propagation affects plant quality - how does this work?

[Fairorchids]

The photos show two markedly different flowers, but the differences are not outside the variables that can be influenced by cultural differences (light, temperature, humidity, watering during bud development & fertilizer).

A true mericlone 'shift' is something that goes beyond these variables. A consistently different color irrespective of temperatures during bud development is one example. Such shifts are easier to identify in commercially grown populations, where you can have dozens (or hundreds) of plants, grown under identical conditions.