The primary difference between the Wall of Flesh compared to every other boss is the context around defeating it. There is an immediate, permanent, map-wide effect upon defeating the boss and the only other boss that does something similar is Cultist, who doesn't have any drops to begin with.
Bosses can be kinda boiled down to this:
Defeated King Slime? Good job, here's a pet for your town.
Defeated the Eye? It'll stop pestering you.
Defeated the evil boss? You can now make a better pickaxe. Try mining more stuff you couldn't break before.
Defeated Queen Bee? Make some room for the Witch Doctor. Didn't get the drop you wanted? No pressure, just fight her again.
Defeated Deerclops? .. what the heck is that thing doing here?
Defeated Skeletron? You can now enter the Dungeon. Take your time, it's not going anywhere. Didn't get Book of Skulls? Did you even want it?
Defeated the Wall of Flesh? There's now an entire new evil biome stretch as well as the Hallow being generated, also both of these biomes spread. Better find them! Oh, there are stronger enemies roaming the map too, so be careful! Here's hoping your Desert isn't evil now, or else you may have just lost it! I see you have Necro Armor on, here's a Breaker Blade and a Summoner Emblem. You can Shimmer the Emblem, but you already have a Phoenix Blaster, so go get em.
The Mech bosses themselves don't drop weapons directly, but they drop crafting materials which the player has control over which weapons they make, if any.
Plantera drops a lot of weapons, but most of them get overshadowed due to the fact the entire post-Plantera stretch has so much gear that the most important Plantera drop is arguably the Seedler for players who wish to craft Zenith, which can be done later on. Alternatively, some players intend to farm her for The Axe, so they're bounnd to get the other drop they care about in the meantime.
Golem drops a ton of stuff, but people mostly want Eyes, Sun Stones, and Picksaws. This diluted loot pool combined with its relatively low difficulty and ease of getting spawn items leads to it being farmed harder than I farm Deathweed, and getting whatever item is wanted along the way.
Pumpkin/Frost Moon bosses are optional enemies that die in such large quantities that skilled players end up getting multiple copies of the item they wanted just a single one of.
Empress and Duke are bonus optional bosses that people often end up repeating just for their Wings, or they fight one of them a single time for their Expert drop and move on with their build.
Betsy is a boss that people end up ignoring, but is often repeatly farmed for her wings and Betsy's Wrath.. but also is from an event that drops its own currency that encourages you to repeat it to get special armor sets.
Lunatic Cultist is the subject of many many threads we've all been a part of so I'm not going to terrasplain this one to you.
So yeah, while the Underworld may not have gotten more difficult to deal with, the overworld has. The surface is one of the key areas to survey where the Hallow and Corrupt biome impacted. While you can just fight the boss again, some players may feel like they don't have enough time to do so because of biome spread, or some players may have only barely scraped by and aren't exactly excited to face the same boss again for what they may feel is their "starter" HM weapon, especially knowing that everything other than Firecracker is likely to be quickly replaced and Firecracker is only as much of a standout as it is because nothing else does what it does to our current knowledge.
I do agree that shimmerable WoF weapons aren't the most elegant solution they set a very bad precedent, but the WoF itself is already a bit of an outlier as far as the game is concerned since it opens up a lot of stuff really fast that, without proper world preparation, has to be addressed on the game's terms instead of when you're ready for it. The fact there is demand for control over WoF's weapon drop specifically while other bosses end up being a "oh well, guess I'll just fight it again" situation is indicative of something, but I cannot for the life of me figure out what since that is outside of my own skillset and without being able to recognize the what it is, I'm definitely not qualified to propose a solution that isn't "throw it into the Shimmer lol"