If you could customize your commander there would be no reason to buy the "new" commanders which are just various mixes of abilities from the other commanders. So I doubt they will do this.
Not if they get creative. DLC commanders could break the rules of customizability, on the condition that the abilities used are carefully chosen.(edit: or even get special abilities not available to predefined ones, payed or not)
If I were Relic, to allow customization of commanders I'd give the player 5 slots, with three options each: a weak but fast options, a balanced option, and a strong but expensive option.
Depending on what option you choose in the first tier, new option may or may not open for the second tier. Some option may repeat, but by doing this, you control how powerful certain combinations are. If you deem a combination too powerful, simply add an extra CP to the next tier's ability cost (so if you mix G43's and Recon run, then recon run becomes a 4CP ability, to balance).
In this way, you can make very strong early game commanders, very strong middle game commanders, or very slow, very powerful steamrolling commanders.
The only real limitation I see right now, is that there's not enough abilities in the game to make a really diverse tree, so even if they had custom commanders, the combinations aren't many.