Pokémon - The Pokémon Mythology Tree

Unown seem like the coding of the universe, like a hidden source code of the universe.
Unown found outside their own realm are like junk data that's been given physical form.

So while Dialga & Palkia created and control time and space, Unown are the rules etched in stone, defining the unwritten laws of the realms. (This is displayed in full effect in the 3rd movie where the unown rewrote water physics to be breathable, turned a young girl's father into a guardian beast & and turned an estate into a huge nonsensical gauntlet. All because she had control of the unknown codebook.)

It is more likely Unown are the metaphorical thousand arms of Arceus. (See, the time in HGSS Arceus spawn for you a legendary egg.)

This is why you can catch/defeat him: you haven't been fighting him at full power with all the Unown as backup.