The only disc I have with two versions is Alien which has a theatrical and director's cut. DVDFab offers me the ability to choose different titles with very nearly the same run time. This would be one way to decrypt and rip only the version you want. If you don't want DVDFab to do the compression, then you'd have to output to a 50gb size.
If you don't have the full version of DVDFab, you should be able to choose the correct title in MakeMKV. Looking at either the full disc you've already ripped, or the original disc, open the index.bdmv file with MakeMKV. Look through the list of titles and find the largest one, which should be the extended version. Right click on the list of titles to unselect all of them, then select the largest one to process.
It would output as an MKV file, which you could import into BD Rebuilder if you need to put it back into Blu-ray format and compress it. If it will already fit your target size, you could use tsMuxeR instead.