I wouldnt say over filtration is harmful per se. I would say an fx6 for filtering 40 gallons is wasteful and the flow rates would be excessive. FX6 flow rate is rated at 925g/h which is a turnover rate of over 20 x the tanks volume per hour. While you wont actually achieve this rate and can restrict flow rate thats a lot of water going through the filter. It also holds around 6 litres of biomedia. In UK money thats going to cost about £75 to fill. You dont have to fill it i suppose, but then whats the point of the big filter?
Compare this to a 407 which is still over filtering to a significant degree. Flow rate will turnover the water just under 10x per hour, which is much more like the number you are looking for with goldfish. Each of the 4 baskets holds about 1 litre of media, you probably want 2 of them holding bio media (maybe 3). So thats about £25 to fill.
TLDR: You can probably make it work, but the only reason to do so would be because you have the filter sitting around doing nothing and you dont want to pay for another more suitably sized filter.