Generally you would be advised to use a homebrew emulator as far more likely to be feature rich, more accurate, deal with quirks and such like
So it sounds like you have an archive file and whatever you are using there is an extractor only.
Size and compression are going to be the main problems you face, and you might not have those. Depending upon the limitations of the included emulator you might face save issues for the GBA games but you could probably work around that
I imagine there is little benefit to compressing the ROMs
That is all the medarot games courtesy of
http://www.advanscene.com/html/index.php , it also notes the medabots games for the GBA (don't think any of the GB/GBC efforts got officially translated,
https://www.romhacking.net/translations/4663/ is the only one unofficially I see and that is PS1, don't think the efforts to do anything with the DS versions amounted to much either but that is not applicable here. One day I will get around to doing Shingata medarot text conversion) which are all the same nominal sizes.
To that end you probably want to find the ROM in the base file. Easy enough if you have the extracted version in front of you to grab some unique data from that, search the big file and figure out where it lands. Compression would be a thing to get in the way though. If you know where it is then try overwriting with the EU/NA versions as you so desire (could also try other GBA games if you wanted). It is not impossible that the files have a hash done to them to make sure they are not corrupt but that would be an oddity for something like this.
If there were different sizes (happens often enough when coming out of Japan, or could even be someone used a trimmed ROM) then you would want to find where the archive lists the file sizes. Hopefully the tool or whatever definitions library it is using is open source to tell you where to look for that sort of thing, however it is also the sort of thing ROM hackers for anything with a file system spend their days finding (and you have the bonus that if it is a unity format you can probably make your own with basic changes to figure it out rather than hoping two versions of the same ROM or within the same rom yields info).
Do also compare the ROMs you dump there with the GBA Scene ones as sometimes these collections fix some bugs, add some extra features or such like.
