Ah yes, the floating reference method! I hate that!
I kind of struggled with the same problem when I was setting up my Mitsubishi cnc lathe. After much head scratching, I came up with a logical method of setting up the machine. Some of this involved changes to certain parameters that required careful study and some trial and error to get things set correctly and logically for my own use.
When the machine homes, do you have a machine position
display? This would be the G53 coordinate system.
Now, pick one of your tools as a reference, typically, I'd suggest an OD turning tool that will never leave the turret, or that is easy to put back in exactly the same position should you ever have to remove it. Ideally, this might be T1.
Now to devise a logical method, I'd suggest that this tool shall be defined with respect to the chuck face. The tool home retracted position is normally where the turret would be parked. Some types of controllers might be set up to call this G53 Z0 at the moment homing is completed, but I'd argue that it makes more sense to redefine that parameter, rather than just giving it a value of zero. Jog and measure the Z length from T1 to the chuck face. If the tool is 16" away from the chuck face, then when the turret is homed with T1 active, the machine position should show G53 Z16.0 I have no idea if you can redefine this by parameter in the controller setup, but its worth a look to see if you can do this.
If you can get that definition correct, then the chuck face is now G53 Z0 and G54 Z is a simple measurement from the chuck face to the end of the part. This can be accomplished with a touch off, or else simply measure the part with a rule or a caliper. Typically, the G54 Z is fine tuned later on anyways, if you need to make a universal adjustment due to stock length variation.
I'd agree that the chuck face is often not a great place to touch the tools off of, so some controllers allow you to define a tool measurement position, just as though the machine were equipped with a tool eye. The tool eye must also be defined relative to the machine coordinate system, but even if you do not have that equipment on your lathe, the parameters can still be of some use.
So, if you made a 3" long cylindrical plug gauge to fit the chuck bore, and that had a shoulder to butt against the chuck face, you could use this as the tool setting reference. Define the length of the gauge as the Z parameter of the tool eye measurement position.
Whenever you have to set a new tool, use the plug gauge as a reference for Z. I suppose if you were to incorporate some kind of a magnetic base thingy, you could affix the gauge temporarily to the chuck face to touch the tools off of.
I don't know if that helps or confuses you more. If you understand the gist of my method, first thing you need to do is understand where your machine is homing now, and what the home position means. If you can, through parameter adjustment, make the home position meaningful to T1, then you have conquered most of the setup problem.