I’ll admit your Fuji looks a little goofy with the tall stem, but it looks exactly like my bikes which I love. So here’s a vote from someone that has this same condition. I have less seat post exposed, but still a tall stem.
I commute by bike, about 15 miles per day, 5 days a week, 7 months per year. I put a premium on comfort. My bikes are comfortable - for me. You and I will be ridiculed for having poor flexibility by people that don’t know us and have never met us, but they’re wrong about me. I just happen to be in my comfort sweet spot with the bars no lower than my saddle.
I ride drop bars with bar end shifters because riding on the hoods is most comfortable for my wrists. I’ve tried various flat bar setups but never found the right one.
When I stand over the top tube of either bike (53 cm Velo Orange Campeur with 35mm tires, or my 1983 21” Trek 500) I’m pretty much scraping the top tube with my crotch. Any taller would be not so comfy.
For about 30 years I rode a larger frame, the next size larger in a vintage Trek. I could never stand over the bar at all - has to lift one leg or lay the bike over. I love that bike too, but it was not good for commuting as I got older, so I got the smaller ‘83 Trek. I shopped for new bikes before building the Velo Ornge but did not find the right combination of fit.
I also do do longer distance riding, 60-90 miles, and solo touring with gear.
We’re all individuals and should ride the bikes we love.