Why should you play DM Machinedramon over purple or black base? Layered interaction. Machinedramon's biggest problem is oftetimes feeling like you're playing gatcha with your cyborgs before dropping the big boy and hoping you got what you needed to break your opponent's board. DM offers multiple forms of removal available every turn with far less investment than the standard supreme connection + attack of the heavy + machinedramon + 5 cyborgs combo.
By playing all of the version 5 cards, you get access to raremon, which is an incredible recovery tool. Just plop him down for 3, and end of turn either go into extyranno for 1 mem, or metaltyranno for 3. Both offer great removal and set you up for either a Puppetmon Ace play, or Machinedramon the following turn.
The Pagumon egg also means that you can swing and digivolve into any ver 5, Machinedramon included from the trash. This means that if you're careful with your facedown card placement, you can pull off some great combos for solid mem efficiency.
The ukkomon serves a vital role in the deck that solves one of DM's biggest problems, getting a digimon in trash. The search is great of course, especially bc DM's searching power is weaker than other decks, but having a digi in trash means you can activate easily in the early game.
Even though this is a Machinedramon deck, extyranno is going to be doing a lot of the heavy lifting for you. It's cheap evo cost + great removal that you can activate on swing with pagumon is so good for keeping opponents from establishing early game boards, and is the deck's only consistent tool against Royal Knights, Kaguyamon, etc.