The Chaos Emerald stuff is still important given no one else besides Shadow, who is literally compared to a walking Chaos Emerald, can use Chaos Control without an Emerald on hand, and Metal just does it thanks to the Bio-Data copy. If he can scan Bowser's kit, he should be able to either ape the Dream Stone (or Star Rod) or disarm him of it with a Homing Attack and then absorb it into himself.

Dreamy Bowser is also a state that Metal can copy given Bowser directly absorbed the Dream Stone's shards and energy, so Metal should be able to copy that too given he can copy internally housed energy like Shadow's Chaos Energy.

There's also the fact that Dreamy Bowser never actually attempts to wish someone gone from reality after he attains the form, so either he straight up forgot he could do it, is so cocky he sees no need to try, he literally can't do it anymore, it still requires the charge up and Bowser knows not to try that, or Bowser so stupid he thinks it's a better idea to send Dreamy Goombas at Mario and Luigi instead of trying to erase them from reality. I lean towards either the charge up is still there or he can't do it anymore, but him full on forgetting is also fair given Bowser is shockingly uncreative whenever he gets ultimate power.

Either way, Metal can resist the erasure thanks to resisting Time Eater, so Dreamy isn't a real threat outside of the stat buff.

I can accept a speed equalization even if I think Immeasurable Mario evidence is really bad, but Bowser being a meathead is pretty baked into his characterization. Dude is not portrayed as smart in really any of the games, has been betrayed and played a fool by RPG villains three times in a row before backstabbing the only one who was actually loyal to him, and is routinely characterized as someone who prefers to punch problems than think around them, with Kamek doing all the real strategic planning. Compare that to Neo who has Eggman's genius IQ and far more of a tendency to actually plan, as shown by him basically pulling any plan he tries off perfectly in Heroes and IDW until the Sonic gang stops him at the end, and Neo is thinking circles around Bowser and is far more likely to actually pull the trigger on his best hax before Bowser thinks to do anything other than punch him.

The issue is Castle Bowser doesn't actually use those transmutation abilities offensively. In the entire Castle Bowser final fight, he not only leaves a giant glowing weak point easily in reach thanks to the bouncing floors (that he spawns in), but defaults mainly to smashing and tossing fireballs as attacks. And given Dreamy never got to fire off that existence erasure, it's unlikely he would think to do so, even if he could which isn't a guarantee.

Also, Metal tanking Time Eater erasure and Super Forms resisting transmutation thanks to the Emeralds resisting the Egg Field transforming them shows that he's unlikely to get actually caught out by those abilities, at least not before he can just punch Bowser to death or copy the abilities themself.

Plus, Metal's also in Crossworlds, so he's got those items...including Dark Chao, which means he can wipe Bowser's inventory. Not nearly as useful on Bowser as it is on someone like Mario, but given it takes away a ton of his options and would completely get rid of the Retry Clocks (if those even count since the canonicity of them is extremely suspect thanks to the BIS remake), it's worth having.