I've tested this on the current stable version (5.3.6) and the bleeding edge version (5.3.8). If I do a first-start of Lucee with an lco file in the server context's deploy folder, Lucee will error out on start up and in some cases, will error prior to installing all the core extensions. This will leave Lucee in an invalid state since not all the core extensions have been installed, but Lucee will never try to install them again.
Placing the lco file in the patches folder prior to starting the server for the first time, does not result in an error.
Here is the startup error on 5.3.6
Here is the startup error on 5.3.8
I've checked this ticket with both 220.127.116.11 and 18.104.22.168-SNAPSHOT of lucee version.
It throws an error while startup in both 5.3.6 and 5.3.8.
But 22.214.171.124-SNAPSHOT throw an error as you said
and 126.96.36.199 throw an error as something different.
And for me, no changes occurred in extension. Seems, all the core extension are installed as normal.
Whether or not the extension fail to load really depends how on fast your server is. If the server errors out prior to all the extensions loading, then you see the behavior. I have a client who hit that regularly in their docker images where about half of their extensions never installed. I assume their containers were slow enough (and had a mix of custom lex files being installed as well) that the controler thread managed to get to the lco file before all the core extensions had been installed.