Yes the color will darken over time.
The wait time on my API tests are 5 min.
I feel that doing exactly as the instructions say will yeald a solid result.
Most dont take the time to do it right.
I know a person who justs adds reagents shakes and done.
Always complained about how inaccurate they were.
I said well your not following the instructions, he laughed and said he did not have time for all that.
We did it the right way as the instructions said and got real results go figure.
I agree that color comparison tests are somewhat hard to decipher but they will show you if your in trouble.
So to answer your question if your instructions say to read at 3 min then I recomend you do so.
This holds true if you bring in your water to be tested at the LFS.
Most dont have time to do it correctly nor do they have clean equipment when testing.
My LFS told me they keep the salinity at 1.025.
I have sampled their water twice now and its at 1.020