There are a lot of answers to your questions and I'm sure that there will be folks who disagree with mine.
First the applicable code doesn't specify any of the things you mentioned. They are all the adaptations of individual engineers to try to address specific issues in specific facilities.
1. The code does say that you must provide over pressure protection that will handle all the credible scenarios and prevent exceeding the overpressure limitations (10% for most cases). Sometimes your most likely scenarios will have vastly different relief requirements. It is common to size a PSV for the smaller scenario and set it at or below MAWP, then size another PSV for the bigger scenario and set it below the allowable overpressure. Since lifting a 6X8 PSV in a thermal overpressure scenario would dump far more fluid than required, this can be a really good idea. On the other hand setting two PSV at the same pressure is pretty stupid since both of them will have a tolerance and you never know which one will open. If you only have one credible over pressure scenario or all of them have similar relieving requirements then you should generally provide the protection with a single valve (no installed spare).
2. Generally, you put a rupture disk under a PSV if you are worried about your fluid being inappropriate to hold stagnant against the PSV (e.g., if the fluid has significant scaling tendency, is very corrosive, or is poisonous). If you have a rupture disk under a PSV then you need to reduce your relieving capacity by a percentage laid out in the code. I never treat a rupture disk as isolation. If I only have a rupture disk under a PSV then I'll depressurize the vessel before pulling the PSV. If I want to leave the vessel in service then I'll have a lockable block valve under it. Block valves on the PSV outlet are a specific adaptation to flare headers--they allow you to test a PSV without exposing the operating personel to the other streams that may enter the flare header.
3. Bypasses leak. It is unfortunate, but it happens. If you have a vessel operating at a very low pressure with a PSV going into a flare header, then another PSV opening can cause the direction of the dP on a bypass to change which will put fluid from the flare header into the low pressure vessel. If this is intolerable, then it can be pretty much prevented by venting between a pair of block valves. When you think about it, a "PSV bypass" is simply a method to blow the vessel down into the flare header. May be needed for operational reasons, but they are never "required" by code.
David