Actually, if you are running your tank on a nitrogen cycle - what we refer to as a "cycled" tank, the ammonia that the fish produce and the ammonia that comes in the water already as yours does, are all treated by the beneficial bacteria in the same fashion - it is all processed into nitrites and then into nitrates.
For example: In tank one, the fish produce 10 units of ammonia a day. It is processed into 5 units of nitrite every day and then into 2 units of nitrate (ficticious numbers). You would end up with 2 units of nitate.
In tank two, the fish produce 10 units of ammonia a day, but the water came with 10 units of ammonia also. It is processd into 10 units of nitrite and then into 4 units of nitrate.
The big thing is, though, it is PROCESSED. If you build a robust enough colony of beneficial bacteria in your filters, they can process the fish's waste as well as anything that comes in the water without problems. You will never even know that the excess ammonia is there - except that you will end up with a bit more nitrate in your tank each week than you would had you no extra ammonia.
As far as the charts of what ammonia is "ok" for a fish, yes, .25ppm ammonia is quite "harmless". But that is also like saying that a little bit of smog will not hurt you. This is true - but anyone with compromised health takes it harder. And some have difficulties no matter what. Add into that, a life spent in an environment that is never as clean and "healthy" as possible, will add up to a degree..... It is always worth it to figure out WHY you have readings of ammonia or nitrite in a tank, and to remedy it as best as possible.