Amplifiers are typically high impedance devices, capable of accepting both high and low impedance signals without any change in tone - they don't care if you are using buffered or true bypass. If you notice a difference in tone when running through your pedal in bypass mode vs. plugging directly into the amp, the change is likely due to your cables or the design of the bypass circuit (or a weak battery in a buffered bypass pedal).
=== Guitar Electronics ===
Most people don't pay a lot of attention to this part of the signal chain, but it can have a large bearing on tone. First, let's get the bad stuff out the way. Bad solder joints will lead to a crackly signal. Dusty potentiometers will sound noisy/crackly when turning them. Improper shielding will allow hum and other interference to get picked up and infect your signal. A good electronics cavity sounds quite a bit better than a poor one.
But there are also tonal considerations for the resistance of your potentiometers and capacitance of your tone circuit. Usual values for pots when using passive pickups are 250K, 500K, and 1M. The higher the resistance, the brighter the signal will be. Lower values allow higher frequencies to "escape" to ground. The capactitance value of the capacitor used for your tone knob will determine the range of how much high-end attenuation occurs. Smaller values will be barely noticeable, only slightly dimming the highs; while high values will result in a very dark tone. The most common value is .047μf.
Be very careful when switching from active to passive pickups or vice versa. Actives usually have much different ideal values for pot resistance and capacitor values.
=== Boosts and Frequency Response ===