any form of effect is going to affect the natural tone, especially the few pedals stated.
But from another point of view, the transparency of the drive tone can be compensated from adjusting the amp(Combo amp at least) eq and the pedal eq knobs.
And for the lilltle colouring of tone, IMHO, boss pedals will alter the tone just that little bit, but it's not a bad thing at all. More importantly, the amp is the deciding factor it....