Why would they not use a higher value capacitor if that improves the sound and provides more pairing options? Cost can't be the reason since the price differences is not much. There must be other reasons or design tradeoffs.You are correct. The bigger the cap, the more coloration it will impart, regardless of the dielectric. As a result, you want the smallest cap to do the job right, if low coloration is your goal. A 0.47uf cap sounds noticeably better than a 5.0uf cap; capacitors are wound on a machine so they have not only capacitive qualities but also inductance and resistive qualities as well. The dielectric (Teflon, paper, polypropylene, etc) affects the sound as does the length and diameter of the part.
This is the main reason that some tube preamps don't play nice with some solid state amps. The coupling cap is too small, and one big enough imparts more coloration than the manufacturer is willing to accept. So the manufacturer solves the problem by declaration (example: ARC limits their preamps to power amps with 30K or more input impedance). We solved it by direct-coupling; others use output transformers (which have a different set of issues).