Quite the opposite experience of dropper posts for me. I used to think nothing of riding for 2hrs with my mtb saddle completely slammed, never ever even thought of sitting down while descending and rode a lot of BMX. My core fitness was my biggest strength and never ever felt knee pain. Fitting a dropper was a huge mistake, for one thing 125mm below optimum pedalling height is nowhere near as low as my usual slammed saddle height and just gets in the way riding very steep technical descents or jumping. But worse than that, the ability to raise the saddle on the fly made me very lazy, to the point I even found myself raising it mid descent. My core fitness and strength suffered and BMX began to hurt my knees much more.
Dropper post is removed again now and will only be fitted for rides where I feel there will be a real benefit from now on.
To answer your question though, YES you will become stronger the more you ride stood up, sounds like you never did this enough with your saddle at full height anyway. Do you ride a full suspension bike? I find a lot of riders use their suspension to aid sitting down comfort rather than utilise the extda grip,stability and tracking that it’s designed to give.