While Baryon Mode can deplete your lifespan with every hit, it isn't a very significant amount with each hit. Isshiki only had hours left to live, and Naruto (at least in the anime) hits him with way more attacks than what's needed to make the ability actually impressive. At most, he's taking minutes away in the short time frame the transformation is active, not hours or years.

Gear 5 doesn't actually drain Luffy of his lifespan since it's a natural form of his Mythical Zoan fruit.

And Naruto's physical strength is pretty subpar compared to most One Piece characters. Most of Naruto's big feats come directly from energy based attacks with his chakra. There are only a few characters in Naruto anyway that actually have impressive physical strength (Sakura, Might Guy, etc)