Just superficially from google images, a Pharaoh bypassing its very mediocre Alps RK27 volume pot (i.e. unity inputs) looks a LOT like the Medusa topology - both have a pair of the same Hypex UcD 400 modules (older than nCore in the new Dragon), a couple large coupling caps, and a pair of 12AU7 tubes. But there appears to be different kinds of coupling caps used over the years in both models. Your Pharaoh, being a current product, may utilize the better (at least more expensive) Mundorf EVO caps that don’t seem to appear in the Medusa (those look like Solens, but without the usual label). It’s quite possible that your system favors one cap over the other. Second, the Medusa very clearly sports input transformers (again, maybe CineMag or Jensen depending on vintage). The Pharaoh DOESN’T show input transformers, unless they’re hidden under the front board which is unlikely. The input transformers alone could be elements that don’t gel with your system - for example, I strongly suspect the Lundahl in+out transformers in the current VAC preamps may be the reason they don’t totally gel with my Tannoy system, whereas the VAC amps (no Lundahls) do spectacular work. So it’s entirely possible that the Pharoah is a much better match for your system, confirming your listening results.
So how did you arrive at the conclusion that a Medusa would be an upgrade? The Pharaoh is a more recent Rogue design, and at a similar price-point to the Medusa, so I think it’s unlikely someone at Rogue would recommend that move. The Dragon has replaced the Medusa, and THAT would be what you’d have wanted to consider for an upgrade. It uses the newer and improved nCore modules, which are measurably higher power and lower distortion. The Medusa has absolutely no power/distortion advantage over Pharaoh.
And sure, you could probably tame harshness and glare with Mullard 12AU7 (especially NOS, but maybe also Russian re-issues which have become quite good), but that will be more like a band-aid if you’re trying to correct for a downstream problem or mismatch. Mullards are warm and smooth with a slightly muted top-end, and some audiophiles abuse them for this reason ;)
One last thought - I always hated the 12AU7 tube in general, and with any Rogue gear I've owned (since they like to use that tube), I immediately replace them with 12BH7. But 12BH7's draw twice the heater current (0.6A vs. 0.3A), and I think Rogue says "not to" do that sub anymore lol.