There are reasons, but just ones that you don't agree with or haven't thought of. You need to understand that reciprocation is in the culture, and people are not purely rational economic actors. It's entirely possible some towns would outright refuse 'assistance' without being able to reciprocate somehow.
Where does the reciprocation ends? You give money to your hometown because you have very found memories and you feel grateful about the education etc., your hometown sends you plums, you send a pie to thank the plums, then they respond back with something else, ad infinitum.
But more practically speaking, from the perspective of say, the mayor of a town in Japan - he has revenue being conciously directed towards him from mostly anonymous citizens of the country. Reciving a real (monetary) gift from someone you hardly know definitely would require a reciprocation. In some ways, sure, you're reciprocating to your hometown for your education/etc, but it's not being seen that way from the town's perspective.
There's also the factor that the redirected tax revenue is a physical thing, where as the 'education and life experience' imbued upon a child growing up is a rather non tangible gift .
There's of course a cynical tax play here. But it is entirely possible that people also _feel good for helping their hometowns_. Sure, there's the vouchers, but there are also the (not super resellable) plums!
It's maintaining emotional bonds in the community. At least that's the most optimistic way of thinking about it
The town I grew up in, Boston, receives a christmas tree every year from Nova Scotia due to the fact that Boston sent a lot of emergency aide to Halifax and the surrounds after a large explosion there in 1917. Something similar could be done with small towns sending local art and culture items to large cities in free exhibitions to demonstrate what the tax money is benefiting or just as a gift or maybe a small japanese town might sponsor a fair in Tokyo where free plums are available using a portion of the tax money they received. This would be a way to express thanks in a common manner for the sum of the donations made by citizens without creating perverse tax loop holes that are exploited to simply lower the amount of money coming out of your pocket.
Certainly it is a (somewhat mitigated) loophole that can be exploited, so in that respect it is not good. But weighed against the positive impact for the rural towns and the connection it makes back to hometowns, you could argue it's worth it.