I might have found a stable way to limit Windows 98 to use only 1Gb of RAM with HimemX:
Install Windows 98 with 1Gb of RAM or less;
Download himemxfrom https://sourceforge.net/projects/himemx/;
Extract himemx.zip and copy himemx.exe to C:\Windows\ under Windows 98;
Open the Run dialog box (Windows + R), type sysedit and press Enter;
Open the file C:\CONFIG.sys;
At the very beginning of the file, add device=C:\WINDOWS\HIMEMX.EXE /MAX=1048576;
Save the modification;
Shutdown your system;
Install the 2Gb of RAM;
Start the system;
Windows 98 should now only have 1Gb of RAM althought 2Gb are installed and it should still be stable.
You can also add MaxFileCache=524288 under [vcache] in system.ini to ensure that Windows 98 doesn't eat to much RAM for its cache.
Limiting RAM to 1Gb with HimemX seems like a stable fix, but I couldn't get the 2Gb of RAM to work under Windows 98. But it still enables use of 2Gb of RAM under another OS in a dual boot setup.
P.S: If there are no answer posted in the next few days that explains how to fully use the 2Gb of RAM under Windows 98, I'll mark this one as the answer.