Just had the same question, did not find an answer anywhere so had not choice but to try it our myself.
The answer is: Yes, you can modify your project’s Config/DefaultEngine.ini file with the values you want, and it will automatically override the existing values of BaseEngine.ini in Engine Directory (for this particular project).
just add the following lines in your project’s Config/DefaultEngine.ini:
When I try to package game for Android I got following error after adding the line to the DefaultEngine.ini in the project:
UATHelper: Packaging (Android (ASTC)): ERROR: UnrealBuildTool.ConfigCacheIni_UPL+IniParsingException: Mismatched brackets when parsing section name in C:\WORK\MyProjects\ProjectX\Config\DefaultEngine.ini, line 142: [/Script/OnlineSubsystemUtils.IpNetDriver] ConnectionTimeout=10.0