No, this is like in GC2 when a survey ship found an anomaly that improved the repair rate of all ships in your empire, except that the description says it affects all of the ships in the "fleet".

"The Fleet" can also refer to all the ships in the Navy, not just e.g. the Home Fleet or some smaller collection of ships. Also, any upgrade simple enough to apply to a ship in deep space with only its crew available to perform the work is simple enough to get applied to every ship in the Navy, and if it's "+2 speed units" then it's also worth applying to every ship in the Navy. It's also difficult to argue that this stuff is supply-limited, since the only such limit is that all the vessels that it gets applied to are within the same group (a possible justification here could be if it were an unstable fuel which is better than whatever stuff gets used normally, assuming that GCIII ships move on reaction thrusters, and have the stuff be so unstable that it won't last more than a turn, but then the +2 moves or whatever would need to be temporary), since the group size can vary considerably.

Well, if you really want to get pedantic about using game-terms, then the game interface never actually refers to the group of ships containing my survey ship as a fleet because I never group my survey ship up with any other ships. Since my survey ship is never part of a specific fleet, any upgrade found by the survey ship which gets applied to 'the fleet' can only be referring to my entire Navy, since there is no other 'fleet' to which my survey ship belongs.

I don't disagree that getting permanent fleet-wide speed boosts from surveying anomalies could have balance issues in larger maps (using 'fleet to refer to the full Navy), but on the other hand several of the other anomalies have the potential to be rather unbalancing themselves, particularly on smaller maps in the early portions of the game. It's also something that can be dealt with by e.g. placing a limit on the size of the speed bonus, which is rather easy to understand as a technological limitation of your faction - maybe you could theoretically get a ship up to 100 moves per turn based on these anomalies, but the spaceframe can't handle that kind of acceleration, or the ship would burn too much fuel, or maybe you don't have a fuel with a sufficient energy density to pull it off, or something similar of that nature. On the other hand, balancing something like 'the last 5 anomalies I've explored have all been Lost Cutters and it's still early enough in the game that you don't have any military technology to fight me off, and I know where all your colonies are' is a rather more difficult problem, especially for early-stage games on small maps.