Maybe.
If you're that concerned about impedance, you must be working in the 20GHz+ range, and with high precision (< 1dB error). In that case, you're probably using Rogers something or other for substrate, and any discontinuity or loss will cause problems. Solder mask and silk should be clear of all such signal paths.
If you're doing any less than this, then no, it makes absolutely, positively no difference. And it probably won't even matter to use FR-4. Typical specs for, say, high speed digital signaling are +/-20% impedance, and undershoot consistent with the losses of, say, 30cm or more of trace on FR-4. Very loose specs. A lot of LVDS drivers even support overshoot compensation, making the system even more tolerant of crappy media.
RF work may not even care, up in the low GHz. It's more if you're doing sensitive work (let alone precision, and planar filters and such), you may then want to use a better substrate material.
Tim