I understood your reasoning for the machine type, I just didn't see any real reasoning to giving him machine type attacks, since there wasn't any real attention put into this side of him. He's definitely wood, and his attacks are wood nature so it'd make sense for him to be a Nature type, not to mention the lines that most make sense with him, and his main line, are nature types as well. Nature/Darkness and Nature/Machine could be dual types, but if he were Nature/Machine I'd suggest his machine attacks to be status effects or something, maybe one machine type attack.
I was wondering about types. Wouldn't it make more sense to put them into the categories they're already in?(Nightmare Soldiers, Winged Guardians, DR, Nature Spirits, etc). Just a suggestion but not required.
As for the questions Arc Knight asked, I was curious about those too, and kinda figured DNA digivolution might replace breeding(as there was no breeding in Digimon, they just died and were reborn into eggs again). Getting the other starters might be a good reason to use the quests on the digivice. I would say that'd be a better way to get the other starters. Then again, that'd also mean you wouldn't be able to get more if they DID replace breeding with DNA digivolution. It'd be kinda neat if they added the digivolve/degenerate system from the DS games, but removed the stat increases. Just making it so you could get other digimon with the ones you have. Another suggestion for possible DNA digivolution would be another evolution type. Like how that one pokemon(I can't remember the name) evolves if it has another pokemon in the party with it. That could be how DNA digivolution works. For example, Exveemon evolves into Paildramon if Stingmon is in the party, and Stingmon evolves into DinoBeemon if Exveemon is in the party. Of course that'd make it where you could only evolve one if you had only one of each. This could also help with your Veedramon solution. Make Veemon digivolve into Veedramon normally, Exveemon could be a side evolution(with more requirements because it'd be "better") Maybe max happiness and level 16 for Exveemon, and otherwise Veedramon.
Also, I was wondering, and I know this is me nitpicking, but when you send out Biyomon it looks really weird, would it be possible to make her look a bit better? I'm sorry about that, but it kinda bugged me when I saw it. xP
Also, Crudalis, that site has citations for everywhere it found it's digivolutions. If you look at it, it has a 3 beside Angemon as an Agumon digivolution, and you can follow that to note 3 near the bottom. This says that Agumon digivolve to Angemon on what appears to be one of the VPet games, I'm not sure if that's what it is, but it came from some form of game.