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Tone
,→True vs. Buffered Bypass
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).
=== Boosts vs. Gain ===
Many people like to use boost pedals with full output, even into modern high-gain amplifiers. Boost pedals often do more than simply boost the signal, as seen below. However, the question here is whether it is beneficial to dime the output when used in front of high-gain amplifiers that have no trouble reaching saturated distortion in their pre-amps without boosts. My general advice is to avoid extremes. In some cases things might be different, but I don't think there's any real difference whether you boost via your pedal's output knob or turn up your amp's gain/drive knob. There might be some differences (most likely unwanted differences) at the extremes. But even beyond that, extremes are by nature limiting - you have no further room to adjust if necessary. I would try to get both knobs an equal distance from 50%.
But before moving on, depending on the length and type of cable you use between pedal and amp, you may find you get a better SNR by using max output on your boost. Try it both ways - make sure when you compare that you are getting the same distortion saturation so you don't have a false comparison. In general, the output knob of a boost pedal should be a simple transparent amplifier, having no bearing on the tone of that device.
=== Boosts and Frequency Response ===