This seems like a reasonable way for Element to continue to sustainably fund development. The CLA gives Element unique power to sell exemptions from the AGPL copyleft requirements for these projects. If Element uses this privilege to grow Matrix as a whole, it will be a win overall.
If Element abuses this privilege, others in the community can fork, and then no-one gets special commercial privileges. In the wildest dreams future when Matrix is a dominant protocol, future clients and servers will emerge anyway, and they could have vastly different approaches to licensing and monetization.
It's more important that in the long run open protocols like Matrix flourish, which strongly benefits from at least one well funded development company.