ARGGG! I had this huge post typed up that answered all of your questions, then my login timed out!
So it sounds like the EBS pedals are not completely true bypass - meaning that something in the way the circuit is wired depends on external power to be present for the signal to properly ground. Quite common. So yes, one answer is to power those with a power supply, and yes the other answer is that you could put them in a loop of their own. Use your ear to decide.
The EHX HOG is probably the best TRANSPARENT buffer you can find in a pedal. The BOSS RV-5 is okay, but tends to kill some of the dynamics that tone has… I always find BOSS pedals make the sound sterile, too clean if you will. They take away organic.
Yes MOOG pedals have awesome buffers too, that you can use to control and shape sound a bit. They do add color however, and if that color is unwanted when the effect is off then you will need to use a true bypass loop pedal like you have to bypass it. Don’t let the built in pre-amps worry you at all, they are fantastic tools that you can use for many different purposes such as distortion, limiting, boosting and coloring.
The master bypass pedal is a neat function because you can essentially preset an effect sound, then hit the switch and melt faces. It would be a convenience item to having a large strip of true bypass loops. I use one.
I’ll post about my rig a little later… but the MOOGS are in their own true bypass loop… I even use a small single TB loop pedal to bypass the 101 sometimes because it’s noisy.
I think the Pete Cornish article is a perspective, one that you could find some information in to assist you with troubleshooting your sound. By no means is it a rule or should it be followed - don’t limit your sound and creativity, use your judgment to create what you want.
Cable is subjective, however long runs can change the tone of a passive pickup instrument - long runs being 50 ft plus of medium quality cable. Active instruments do not suffer from this because the output is low impedance, which is what every pedal with a buffer outputs too. Optimize cable lengths, don’t blow the bank on cable, it’s just not worth it. Always remember this when things get out of hand: Jimi Hendrix, The Beatles, The Band all did it without today’s technology, why do we have to. It’s all marketing, and every time one of their songs gets mastered someone takes out all of the recorded “imperfections” and rebalanced the EQ anyways
If we bought food like some people buy cable we’d all be eating organic free range fat free top of the line quality food. Money better spent IMO - makes the brain work better, thus playing better.
Back on topic… I’m running 18 pedals loops included, and have no issues with planet waves cables robbing tone. I have a mix of true bypass and buffered and I (ab)use my amps FX loop.
Buffers vs true bypass is a subjective topic. Try this: Plug your passive bass into the Fuzz Factory, then into your amp. Set the gate at 3 o’clock or more. Let a note ring out noting the sound of the decay. Now plug the same bass into the HOG, then the fuzz factory. Run the HOG in bypass mode and play the same note and let it ring. Note the difference! Now take the HOG out and use your Active bass into the Fuzz, and note the sound. You will be able to hear what a buffer and active pick-ups can do to the sound quite clearly. What works for you is your sound 
I have some pedals in a specific order because the buffers mess with what I want the pedal to do - like react to the pick-up organic qualities.