The problem is I can't submit this since officially (unless someone finds Floppy v1.1) the game was shipped without a working copy protection.
Have you confirmed the bug with an actual floppy version of EcoQuest v1.000, not just one downloaded from the internet?
You're right, random codes are
blocked if you install through floppy installation files. This can be confirmed thanks to the Internet Archive, which hosts eco-quest (that's how this specific archive is spelled, as I probably shouldn't link directly) with 4 ZIP files, one for each disk. It can be installed via DOSBox by mounting a general folder, then copying the files from the first disk there, installing until the next disk is requested, then emptying the folder and copying there the next disk, clicking enter inside the installation to process the next disk and so on. Once done, in both DOSBox and ScummVM (even without the command line parameter) the copy protection can't be bypassed.
This confirms the very reason I've opened this topic in the first place - it means the Internet Floppy v1.000 was indeed
hacked. Not by SCR files though, so I suspect by modifying the RESOURCE files directly. I wonder if the CD version was hacked too, just in a different way.