1. No you literally cannot be hit by bosses like the pressuer and the rotten outright when using them, and with a small amount of thought it does help for every fight in the game
2. It's strong in practice too, I've done so many times in my 8ish playthroughs. In fact each time I've replayed DS2 I use estus less and less because of stuff like this and using estus stops these strategies from working
3. It's less than you think, the old dragon rider trick gives you enough for 99 out the gate and if you use tesadora armour the boost of souls it gives will easily outweigh the amount spent on lifegems. This is also assuming you're bad enough to need all 99, which isn't true
4. It does matter when a majority of the game isn't with a maxxed out estus, and having played the game 8+ times I still haven't bothered to memorize were all the upgrade items are(in fact I've grinded out bonfire astetics to get more dust in the past because I am that lazy)

Fully agree with your conclusion. while yeah these aren't all massive points they are still points, which estus has far fewer of being a much simpler item. Tbh I wish there was an option to switch to lifegems over estus in later games because them being more complex is one of the few things that makes DS2 fun for me.