I'm working with Agfa Apogee since ApogeeX 2.5 (and now it's Prepress 10 version) and I also worked with Kodak Prinergy, Heidelberg Prinect, Fuji XMF and Screen TrueFlow so I can compare some things. And I can say that Agfa Apogee Prepress for now is really comfortable modern full featured...
A little bit senseless question because actually you are not distort not only the art on the plate but the plate itself so if you distort the art = you distort also all marks include bearer marks
Basically it depends from Color Management possibilities in the Rip (and these possibilities depends from APPE "core" version). But if I remember everything right TrueFlow don't have such possibilties at all may be in Equios (current version of Screen so called "workflow")
Unfortunatley, without calibration such plate exchange can give you unacceptable quality results. But I don't understand why calibration is problem for you, because for all Screen CTPs plate calibration is the standard procedure and it can be done by qualified operator in most cases.
It's not good idea to use Brisque in 2017. As you have Lotem 800 II Quantum you can find another "necrohardware" Adaptec SCSI 29160 board, plug it to PC with PCI slot, install Kodak Xpo and have 1-bitt TFF spooler on standard PC platform with modern network and so on
What exact means "workflow will drive our Lotem 800 II Quantum"? Сreo made CS Expose for exposing 1-bitt TIFFs for replacing Brisque workflow and Kodak just renamed CS Espose to Xpo. But Kodak closed support for Lotems and that why they are saying "they can't drive the Lotem with latest Prinergy...
You can start from AE complete manual - http://docs.esko.com/docs/en-us/automationengine/16/userguide/h and read the chapter "Integrating with External Systems". This gives you basic knowledge about using XML in AE.
It's because you are trying to do something as standard user of CP 2000, NOT SERVICE. I will try to ask my client to make photos of screen of CP 2000 to show you.