You seem to be missing the point that Shoddy is not attempting to simulate Pokemon, but rather is attempting to simulate one part of the game. The issue is really not, "How game-accurate should we be," but rather, "Do the PID nature/IV restrictions and Event Moves fall under the part of the game we are attempting to simulate as accurately as possible?"
Therefore it makes perfect sense to be able to draw lines in what we simulate. If we didn't, why aren't we all just playing the cartridge?
Furthermore, there is a large flaw in your infinite time objection: Namely, you don't have to breed every Pokemon you're using on your team. Shortly after their release in Japan, Diamond and Pearl combined to sell over 1.5 million units. This doesn't include later sales or any other country's releases at all. Now, certainly all of these sales didn't go to people who breed competitively online, but it does become much, much more likely to be able to find, somewhere in the world, a perfect IV version of every Pokemon out there than it does in your artificially restricted world of you.
We
should restrict non-breedable Pokemon's Natures and IVs to correspond with game mechanics. It falls into the category of battle-affecting things which we should be simulating in a battle simulator; albeit rarely, minor stat variations will affect winning or losing a match through lack of a speed tie, not quite enough defense/offense to avoid/get the OHKO/2HKO, etc.
We
should also allow Event Moves for which we have decent knowledge of their distribution. Movepool is one of the bigger components in Pokemon viability in competitive battling, and so it is important to simulate 'real' (i.e., not the ditto glitch, but that's a whole 'nother topic) movepools whenever possible.