no messy system or leftovers. some programs use directories all over the place and it gets annoying fast if you host many services. sometimes you will have some issue that requires you to do quite a bit of hunting and redoing things.
docker makes this painless. you can deploy and redeploy stuff easily and quickly, without a mess. updates are painless and quick too, with everything neatly self-contained.
much easier to maintain once you get the hang of things.
i mostly agree except its leagues ahead for sysadmins and devs, it isnt even a contest. to counter your specific example, filezilla works great. i havent used a tool for this specific niche on linux that wasnt much better.
affinity photo is great on linux too if you are not too stuck with adobe. cant say much about other usecases you mentioned.
also wine runs old software better than windows in some cases. i have better luck with it on linux. funnily enough old linux software is a pain on linux in the rare situations where i need it.
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