It’s not flawed, it is absolutely correct, but only under the assumption that you have a competitor. For example for KBP-ODS your flight might be the only connection available in the whole game world. In that case, you should maximise price (while maintaining positive ORS) because it will not affect your seat load. But for routes like AMS-DME, if you want to get a share of connection traffic through AMS-KBP-DME, you will have to keep prices reasonable to compete with not only the direct flight, but also connections (via VIE, PRG, etc)
You should also check your flight pages to see how much of your passengers are from connections, that really help you make good judgements as to which routes to expand, how to price and how to schedule.
Also, my personal view is that if a short haul domestic route doesn’t fill without connections, it’s not worth flying. Connections are extremely important for long haul, but your focus is solely on short haul, so perhaps it is less important for you. Also in my opinion it’s nicer to make connections through good scheduling than competitive pricing.