Joe, I don't see anything "impossible" in identifying John Jenney of Lakenham with John Jenney of Plymouth, although the conjectural scenario, if true, is certainly unusual. In answer to your points:
1. Not necessarily. My supposition is that John Jenney was being treated as an adult, because (1) he was an orphan from a gentle family who was almost of age; (2) treating him as an adult was a lot easier than going through the motions of assigning him a guardian; and (3) he had family and/or friends of family (Homberston, Gonsalves) who were looking after him and informally sponsoring him. Furthermore, "miller" in this case has to mean that he was an employee of somebody else, because he never appears in tax records as owner of enough property to be a mill.
2. The weapons and helmet on the militia record could have been borrowed from whoever was acting as his patron. I don't think the record indicates that he was necessarily the "owner" of the equipment, just that he showed up with it.
3. Hovious indicates that Jenney appears to have filled in as a substitute constable for somebody who didn't fulfill his whole term. In this case, he would have been 19 years old, and if there was already an informal community decision to treat him like an adult, then this further step doesn't seem like that big a deal.
4. In Lakenham, Jenney was identified as a miller but once again it doesn't appear (from tax records) that he was the owner of the mill. A man with such an economic situation would have great difficulty finding a wife from his family's social class, so he didn't get married. The visitation pedigrees are littered with younger sons who "ob. s.p." -- so in this case it would seem an unexpected gift of fortune that he eventually married at all -- in a community of religious exiles in a foreign country, where the social status of his wife wasn't as important.
5. I don't see any problem with this. John Jenney, over age 60 and in good health, accepts apprentices and much of the training and oversight is done by his son-in-law Thomas Pope, whose son Seth Pope and grandson John Pope (both my ancestors) also became millers.
6. As a religious exile in Holland, John Jenney had to do whatever he could. As a miller in England, presumably he had some experience with barrels, which meant that he was able to find work as a brewer's man in Holland, and learned a new trade. Then in Plymouth he was able to do both.
All of this is of course conjectural, but we are brought back to the apparent fact that John Jenney of Lakenham seemed to end up with the property of Avis Jenney as she moved to London with her eldest son, presumably as he came of age.
On the other hand, Avis Jenney's husband Christopher Jenney had a first cousin, a lawyer also named Christopher Jenney, who was the executor of his will. Perhaps Christopher Jenney had a youngest son Henry, who had to get married quickly and had a son John who ended up receiving Avis's property in Lakenham as part of the arrangements settling the estate of her debt-ridden husband. But I have no reason to expect anybody to accept that as anything more than idle speculation.