The system is great because it counters cheese. Without it you could have an offensive player with 49% upkeep, and an economic ally with 0% upkeep, who just harvests the resources and sends them over to the offensive player. They get more total money, and they also get to skip whole techtrees...
The funny thing is the system does not really counter this case, just makes it behave sensibly. If we have an econ player A with 0% upkeep, there is no double tax on his harvesting. If those resources are donated to player B with the 49% upkeep, he still gets to build his fleet with just a single tax, which he would have to pay anyway. The difference is that player A will harvest much more efficiently, and player B can skip whole tech trees, so no. The system mostly hurts the case where both players have real fleets. One quick solution would be to deduct the receiver's tax percentage by that of the donor's.
To a degree econ players are balanced by the fact that with 0 fleet you are pretty vulnerable - the team also loses the player's fleet management capability, because then there is no one to take care of defense/offensives in 1 more location. If the enemy notices (any player worth their salt should!) that one of the enemy players has no fleets, but instead lots of tradeports, refineries, civ labs etc etc, it shouldn't be too challenging to figure out 1) what is going on 2) who is the easiest target for the next attack. And when this player goes down, the whole team will be screwed, because there was just 1 income source not 3. This helps to balance the extreme cases quite a bit.
To me, having a dedicated econ player is a valid tactic, and it just should be balanced. If the total benefit of having a dedicated econ player is reasonable, and there is some kind of a disadvantage as well, then the net effect is that the strategy gives knowledgeable players just a slight edge, and everything is as it should be. However if the player is forced to not build any fleet, that weakens the gameplay and the balance is not where it should be.
For regular players passing RU between each other, that is just regular teamwork, and makes for a good team dynamic when players cover their buddy's (momentary) weaknesses. Of course there is the aspect that this helps the team recover from attacks and other threats, so it will make the games a bit longer when teams can stay on a good footing longer. But as it is, this is totally nerfed to hell and back currently, especially in the late game. With a 49% penalty, donating RU would be reasonable only in rather special and dire circumstances, and could not become a regular catalyst of team spirit. I like the fleet upkeep penalty in general, because it nerfs huge fleets and balances the action (although that again makes the games longer), but in this case it seems too steep a progression considering what would be fun gameplay.