Partially disable SIP on Mac with multiple partitions?

I have a Mac with multiple partitions and installations of OS X. One is running TS on El Capitan with SIP fully enabled. If I want to install TS on another partition with Sierra, and if I follow the instructions to partially disable SIP by booting into the recovery partition, will I then disable part of SIP for my entire system, i.e. all the partitions, or can it be done only for the one partition with Sierra?

Each partition with a bootable macOS installed should and/or can have its own associated recovery partition, but doesn’t always necessarily so. This depends on how the partition was created and the macOS installed on the partition. If you used a macOS installer and installed to the partition, then it should have created a recovery partition for that macOS partition.

If the partition was cloned, then depending on how it was cloned, it may NOT have a recovery partition associated with it. Anyways, to answer your question, each macOS partition can have its own ‘setting’ set via its associated recovery partition. If you hold down the Option key while booting, you will see all bootable partitions on the boot drive. Ideally, you should see a separate recovery partition for each OS partition. Since one OS is El Cap and the other Sierra, you can tell which recovery belongs to which by looking at the version number listed under the Recovery partition on the boot screen. This is the best way to select the recovery partition to boot from when there is more than one…simply using Cmd-R during boot will only select the recovery partition associated with the current default startup drive, i.e. if the El Cap partition is the current default startup disk, then Cmd-R boots to its recovery partition, or visa version if the Sierra is the startup disk. Using the Option Key method gives you control over selecting which recovery, regardless of default startup disk.

whichever recovery partition you boot too, whatever ‘csrutil …’ command you execute, applies ONLY to the OS partition is paired with, thus each OS can have its own setting.

But what if you don’t see a matching/paired recovery partition for your OS partition? Well then it gets interesting. You can google what to do in that situation (create a recovery partition after the fact if OS is already installed). OPtions includine running the appropriate installer so that the recovery is created (your data shouldn’t be overwritten, all it does is reinstall the OS); another is too clone the recovery partition if it exists from the same drive you cloned the OS from; use Carbon Copy Cloner to clone the recovery. and so on.

Not possible AFAIK. SIP flag is stored in NVRAM which is machine-wide configuration.