What option did you use for the setting in ESTLCAM-setup-basic settings-cnc program start?
How did you do it, your exact workflow?
You should be able to home the machine with your touch plate @ Xmm thick, Then make your program with estlcam set to cnc start “above origin” or one of those options. I do not use endstops, but it is very possible, I think you just have the setting wrong. It is how a touchplate works. So maybe some more details, so I understand what you have tried.
Or give me a screen shot of your setttings.