Well given that the ally matrix allows everyone to ally with at least two other armies barring Tyranids, that might not be entirely correct. Consider:
In any given MTG tournament, you are restricted to a selection of cards from the many thousands available (let's assume you're playing Standard Constructed). Some of those may be banned. Most of them will not work in your deck archetype (almost all aggro cards are useless for a control deck, for example), and anywhere between half and two thirds will not fit in because of colour restrictions (with tri-colour being the most you can realistically build a tournament worthy deck from). Of those cards that match both colour and archetype that are currently in Standard, something in the region of 60% of those will be jank that have no place in a tournament deck.
Thus your pool of "potentially useful" cards that you can consider adding to your deck is often in the low tens, rather than hundreds range.
The same idea can be applied to 40K however. If you want to play a specific type of army (say bikes) you will be limiting your self to specific types of units, much like how you be limited by the deck type you wanna play in MTG. Allies function as colors, as you will be looking for the units in the allied books to complement your deck, and you are limited by the number of "good" units that will be used in a dex as some units are just bad. Of course you can still take whatever units you want in 40K, just like you can run 5 colors in MtG, but it would reduce the overall effectiveness of your list (at least depending on MtG block or rule set).
Your actual choices for your list are just a limited, if not more so, then in Magic.
Obviously there is some overlap between codices (Tac squads are basically the same, no matter which book they come from) and there are also some terrible units in each codex, but we haven't even looked at Fortifications, Forgeworld or Apocalypse yet.
Therefore, even if some tournaments end up banning certain units (so far we've got a list of, what, 3-4 units and a wargear item?) there are *plenty* still left to choose from.
Many tournaments already ban Forgeworld/Apoc and have imposed restrictions on Fortifications. Imposing more restrictions on players just further limits options and what lists will show up at any given Tournament.