I think that when they say emanation of Vimalamitra they feel that Vimalamitras qualities are visible in a person, it is not the same as a Tulku.
Khyentse Wangpo can not be the co-incarnation of many masters either.
I think "co-incarnations" are complete nonsense.
however I don't believe Jamyang Khyentse Wangpo is less enlightened than masters who dissolve their bodies into light just because Khyentse Rinpoche didn't show that. If Khyentse can have trulkus, why Jalupa can't?
I thought JKW did achieve rainbow body? But anyway you have a point. Though you have to assume that those masters were indeed fully enlightened. Which is something we can't know for sure, since like you said an ant can't compare the height of two mountains haha.
Ju Mipham Rinpoche claimed by himself that he won't have a reincarnation before his passing. But his trulkus are still recognised by great masters such as Penor Rinpoche.
Anyway, I also spoke to Namdrol about those who achieved rainbow bodies having rebirth and he too said that in the tantras it says they can have a non-afflictive rebirth. This however begged the question if such a one is reborn what's he like? I didn't get an answer on that but my thinking is if a full blown Buddha chooses to take rebirth then he should be a full blown Buddha when he is born. Studying, practice and stuff shouldn't be necessary. Heck if in a previous life he achieved rainbow body if you set him on fire in this one he shouldn't burn. So with that, I still don't believe there is any who achieve rainbow body that take rebirth.
first, I don't think that tulku claimed that he is a Pemadudul's tulku in Tibetan. He is the tulku of a great lama, the son of Lerablingpa, a emenation of Pemadudul according to a terma (I didn't read the text though). So, in a sense, he is one of 'trulkus' of Pemadudul. But he is not formally recoginzed and given name as Pemadudul's tulku. It's like Penor Rinpoche is recognized as previous Penor Rinpoche's reincarnation, but we consider Rinpoche as an emenation of Vimalamitra as many other great masters said.
But the idea of 'Jalupa can't have a tulku' is something I don't really buy. I hope we are not playing words here, because terms like 'emenation' 'incarnation' 'rebirth' all have their limits. I don't think Jalupa will usually have 'rebirth' either, but the term rebirth can not cover the term Trulku.
We don't even have the same idea when talking about 'Jalupa' here. Vimalamitra is a 'Jalu Pochen', Pemadudul is a siddha who dissolved his whole body, many other masters left only small size of bodies are also called Jalupa, and now you say you think Khyentse Wangpo is also a Jalupa.
As you said we don't know if Khyentse Wangpo's enlightenment is equal as Pemadudul's, but then how can you know Pemedudul couldn't have a flesh tulku? We just couldn't know anyway. But I can say there is no base that Jalupa has higher enlightenment than non-Jalupa, otherwise all Jalupa would be higher than Buddha Shakyamuni. Actually there can't be a tantric base saying that Jalupa can't have a tulku (in sense of tulku system's tulku), because the system was created after tantras were formed.
I can't see why masters can't be co-incarnations. If Khyentse can have 5 or 25 tulkus, then one tulku can be from 5 or 25 masters. It's so common in Tibetan Buddhism really. A near case is Shechen Ramjam Rinpoche, who is the combination of Shechen Gyaltsab, Ramjam and Kontrul, according to dilgo khyentse Rinpoche's pure vision. You feel it's non-sense just because you are sticked to one-soul-one-being idea; buddhas are not limited by this.
The question about 'if a tulku still needs to study' has been answered by Jigme Lingpa. Anyway, even Shakyamuni Buddha himself who has been enlightened ages ago, as said in sutras, still appeared to be a common prince and went through all study processes.
Finally, to Heart: what's the difference between a 'Vimalamitra's qualities in visible form' and a 'Vimalamitra's tulku', besides the later one got a recognization letter?