If it can help, I narrowed down some exact strings to replace in the file project.pbxproj to fix the problem. With these swaps, it was not necessary to check carefully anymore and I can automate the process.
Note: Xcode_project represents the path up to the Xcode project folder.
Note 2: in Notepad++, I had to uncheck "match whole word only" for the program to recognize some strings.

$(SRCROOT)
$(PROJECT_DIR)
$PROJECT_DIR
All three replaced with
C:/Xcode_project

$CONFIGURATION_BUILD_DIR
Replaced with
C:/Xcode_project/build/Release-iphoneos/GameAssembly

path = Il2CppOutputProject/
Replaced with
C:/Xcode_project/Il2CppOutputProject/

path = Libraries/
Replaced with
C:/Xcode_project/Libraries/

"Il2CppOutputProject
Replaced with
"C:/Xcode_project/Il2CppOutputProject

"Libraries
Replaced with
"C:/Xcode_project/Libraries

These replacements were sufficient for my app to be built successfully. No guarantee for others though.