Depending on what options you are checking in Boot-Repair, it renames the windows efi files to a backup and installs shim. When Boot-Repair says to boot with shim, it probably should just say ubuntu from UEFI menu as that is what UEFI will show. Or if only able to boot Windows the shim file may really be named the Windows boot. See below for more explanation.
But there really are 3 main efi files, grub's shim which includes the "key" which is the Microsoft key to boot in secure boot mode, the standard grub, and the Microsoft efi files. But only those systems that only boot from the Microsoft efi file is where Boot-Repair will rename the Windows efi file and use the shim file. Then when booting from Windows entry in UEFI your really get grub menu and from grub menu you boot the Windows backup.
If system will boot ubuntu entry you have two choices. The shim should work with secure boot on or off. The standard grub will only work with secure boot off. Then you do not have to rename the Windows file and copy shim into the Windows directory.
How Boot-Repair fixes a Ubuntu with grub-pc with efi Windows
Boot-Repair - Updated Jan 1, 2013 to not rename first time, but rename if first time Windows does not boot. Post 706 and 711
Boot-Repair copied /EFI/ubuntu/grubx64.efi to /EFI/Boot/bootx64.efi (in case the BIOS is hard-coded to boot into /EFI/Boot/bootx64.efi or secure boot
signed GRUB file shimx64.efi.
Depending on how you view efi partition these are the files used for booting. Normally from Ubuntu the efi partition is mounted at /boot/efi so you may see /boot/efi/efi/ubuntu for example. If you see files with bkb then Boot-Repair is making backups and renaming files. Always best to have full backup of efi partition as it is vital for booting.
# UEFI Boot files UEFI sees folder for efi files, so it will show, ubuntu, Windows, Boot and maybe others for recovery.
# for grub/ubuntu
# New secure boot grub version:
# for Windows, but for UEFI systems that only boot this file, grub or shim may get renamed to this and this backed up.
# Both Windows & Ubuntu may provide this shell file, not sure of differeneces.
# There also may be other files in each directory to support booting.
If Vendors would correctly implement UEFI, even with secure boot we would not have all this hassle of renaming files or having to do other work arounds. Only a few computers seem to work correctly, many need the work arounds, but then that often complicates the install process for everyone.