How to properly use a transformer which bundles its high & low voltage wires together?
I'd simply take this transformer back and get a different one
The transformer you have was designed for use as a replacement transformer inside HVAC equipment, hence the design with primary and secondary wires in the same nipple.  However, this also means it's RU (UL Component Recognized, or Rather Useless to us) instead of being UL listed, which isn't helpful in our situation.  I'd take this back and get a different transformer with a full UL listing and a different wiring arrangement; in the Johnson Controls lineup, the Y65T21-0 or Y65T31-0 would be suitable substitutes, depending on the mounting arrangement you're working with.  (They also provide an extra &quot;blind&quot; terminal on their secondary side that can be used as a general wire-connection point.)