The new file system is
not optional for an SSD and it is not compatible with Time Machine unless my information is wrong/out of date.
If the install is invoked manually using the terminal method it will -NOT- touch the file system. I have plenty of high Sierra installs on SSDs formatted GUID Partition Table / HFS Extended format.
It does not ever do anything to any other volumes on the system. Ever.
As for Time Machine, the only issue there is that the Time Machine where the backups are placed can not be APFS. An APFS volume can absolutely be backed up/restored with Time Machine, The root cause being that APFS does not support Hard Links and that is how Time Machine organizes access to unique entries.
Hard Links are a method of "aliasing" where there is more than one entry pointing to the same data in a file system. If you have Hard Link entries, the data occupied by the file will -NOT- be recovered as long as any other Hard Links to that same data are present. Where as with a Finder Alias, (Symbolic Link) you can delete the actual file and have any aliases remain as broken links.
The method that the disk is mounted is not relevant to APFS optimal performance. (USB, SATA, Firewire etc..) Rather it is the medium. Flash/SSD volumes that are used strictly with Apple devices will benefit from APFS. Otherwise leave it alone.
Again, the -ONLY- time when file system conversion is even an issue is during an INITIAL install/upgrade, and will only happen if the volume is electronic based, unless the install was started with --convertoapfs NO enabled.
Likewise, the opposite is also true. You could force APFS on a volume during a High Sierra install/in place upgrade by specifying --converttoapfs YES .
That is the only time ever. Any Software Updates, e.g. 10.13.x to 10.13.x will NEVER change a file system.