If you use gparted to disable your existing EFI partition prior to install, and 
if you have followed the advice to create a gpt partition table and an EFI 
partition, you can work around it. 
After the install, use gparted to reflag your internal EFI partition. 
This worked for me with Ubuntu 18.04 on a new Thinkpad t480 dual boot, with a 
new install to a thumb drive. 
https://askubuntu.com/a/1056079/152287

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https://bugs.launchpad.net/bugs/1396379

Title:
  installer uses first EFI system partition found even when directed
  otherwise

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