Re: Boss pedals
All Boss pedals have buffers before and after their effects section, with FET transistors doing the bypass switching function. Sometimes the FET circuit doesn't really "bypass" anything, it just shuts off the wet signal. The CE-2 chorus is this way - the dry signal goes through the buffers and an op-amp stage all the time, and the chorused wet signal is either added to it, or not.
To many of anything can screw up your tone. Heck, even the plugs, jacks, and cables have an effect. True bypass pedals puport to get completely out of the way when tney are in "bypass". The problem comes when the effect in question is signficantly different from the straight-through path in terms of impedance or level; that is, the way it interacts with the pedals on either side of it.
Buffers are designed to sort of level the playing field, to eliminate the interactions, or more accurately, the big changes in those interactions that result from switching true-bypass pedals in and out. Some combinations of pedals interact well, and others don't.
Case in point, my MXR reissue Phase 90. It sounds awesome, but it's a tone sucker. As it came from the factory, with an authentic old-school non-true-bypass SPDT switch, it sucked tone all the time. Now, with a true bypass switch installed, it doesn't suck tone when it's off, but it does suck tone when it's on. So, there is a step change in the amount of tone suckage when I switch it on.
Is that good or bad? That's up to the player to answer. Since it's not one of my core pedals, and I use it infrequently, I decided it's better to "get it out of the way" with the true-bypass, and take the hit on tone suckage on the few occasions I use it. Another player, one who uses the phaser frequently and switches it on and off a lot, might decide it's better to 1) leave the tone-sucking SPDT switch in place and compensate for the tone suck elsewhere in the chain, or 2) use a buffered phaser that doesn't suck tone as much. Our own ErikH actually added a buffer to the output of a Phase 90 to eliminate the tone suck.
Also remember (and this is where it really gets complicated) that with a bunch of true-bypass pedals the interactions between pedals move around. That is, the "adjacent" pedals are not necessarily those wired on either side. In terms of pedal interactions, the "adjacent" pedals might be several pedals down the line, if everything in between is true bypass. Turn one of those in-between pedals on, and suddenly it becomes the "adjacent" pedal. The permutations can be mind-boggling.
Right now, my pedalboard has 5 buffered Boss pedals and 2 true-bypass. Sure, the 5 buffered pedals have an impact on tone, but it's a consistent impact for which I can compensate with my amps volume and tone controls. No one solution is right, though I venture to say a well-thought-out mix of buffered and true bypass is probably the best solution.