The way to get the same effective seat height on different bikes with different seats is to adjust to the same knee bend. Sounds hard to do but it isn't. First, get the bike with the seat height you like. Bring it indoors and lean it next to a wall. Put on shoes with low heels, like typical cycling shoes. Get on the bike and sit in your usual riding position using the wall for support but having yourself and bike as upright as possible. Rotate the wall side pedal down. Now, put your heel on the spindle of the upside down pedal. Do not rotate your hips to reach the pedal! If you cannot reach, find a pair of shoes with enough heel that your heel reaches. Now, can you also bend your knee a touch without lifting your heel off? Does your heel lift off? Get another pair of shoes with again touch more heel or if it is really close, put a cardboard "lift" inside the shoe under your heel. There is a magic amount of heel that will allow both contact with a straight leg and contact with a slightly bent knee. (Remember, this whole time you are keeping your hips level. If you cannot straighten your leg, go to a shoe with a smaller heel/thinner sole or even go barefoot.)

Yes, it took a little work to establish your "baseline". But now, you can put that shoe on and quickly dial in any bike. Get that other bike. Adjust the seat height to that magic place. Done. (Now, different types of pedals make this a little more complicated as your foot height may change. Might take measuring your shoe on the pedal and compensating the seat height accordingly. Or having an outside observer measure down from a mark you make on the ball of your ankle to the centerline of the pedal spindle.)

Knee issues - as well as seat height, tight hamstrings can cause them as can improper foot position on the pedals and not keeping them warm enough. I've been dealing with knee issues for 40 years. I ride with a lowish seat (I do the test above in my socks, no shoe) but I have to stretch, I have to have my cleats set right and I have to keep my knees warm. I was told by an orthopedic surgeon when the symptoms showed up that not doing those things meant investing in third party replacements. Since then I have ridden 150,000 miles and still have my originals.