The rot pocket is constantly trying to heal itself so the smell may always be there..
The olfactory systems of any animal will slowly 'unregister' bad smells which they're routinely used to over time, the term we usually use is "Nose blind" to define it, this is a basic bit of biological defence because how can you sense chances in your environment if you were always aware of the worst smell? This would be incredibly inconvenient for something like a dog which gives off a lot of different smells itself which're often overpowering or disgusting to us (With a weaker sense of smell). So regardless of "Well the smell is always there" the brain of any animal which relies on it's nose for guidance in the world will "filter" out smells which are always in it's environment for smells which may be new. If you want this simplified consider how someone who is a hoarder living in a pit of house can have millions of cats who don't mind living in the filth (Despite cats having a heightened sense of smell) and sometimes dogs who similarly don't care.
Again, I would argue the problem isn't "Dogs/cats smell the wounds and reject them due to it", otherwise dogs around people who're recovering from surgeries and the like would display the same behavioural quirks. The idea it's due to changes in hormones (so our natural body odour by proxy) and changes in appearance/deodorant and bodywash usage might play into it is tenable as these things do not happen overnight, it's a long drawn out process a dog would likely adapt to over time due to how slow and drawn out the change from "I'm a guy" to "I'm a troon" realistically is, it takes years and none of it is a snap of the fingers and you're done. Again, if it was as simple as that which would confuse a dog and make them aggressive, you'd never be able to change your perfume/deodorant without your dog going batty because a new smell is in the mix, or if you decided to cut your hair from long the dog would suddenly get aggressive because you're a new person. Doesn't work out that way.
To re-iterate, as someone who has trained dogs, even dogs who show violent tendencies towards men, it's all about how you act around the dog down to the ground. If you spend your time staring it out and being nervous/afraid of the animal (Or if the owner/alpha the dog takes cues from is nervous or shows signs of fear when you're around) it will become defensive and aggressive, it doesn't understand the nuance only the primal instincts the situation evokes, they perceive you as a threat and that's the end of it. But if you literally pretend the animal isn't there (And also, if the alpha/owner of the dog does the same) the dog will be calm and completely fine with the situation, even if the person is completely brand new if they act with confidence and the owner does to, you're all good.
With troons in particular who's entire world view is "Everything that isn't with me, is agin me", they see any slight from anything as an attack on their identity and will become defensive/aggressive and react by becoming anxious/nervous as a result. When you're around an animal which goes off of 'vibes' like a dog, it will lead the dog to react in kind. If they weren't so busy thinking the dog has such complex social apparatus as gender-based bias towards another species and just literally acted toward the dog like they did before, they'd be perfectly fucking fine.