You can if you want and easy to try. It can be hard for code to identify all records that should merge, but if you are confident you want to merge above some score (say 95), then insert this code:
if merit < 95. :
choice = GetOption(prompt,msg,["Don't Merge","Merge","Cancel"])
else :
choice = "Merge"
To insert it, open the MergeRecords.gplug extension in GEDitCOM Editor (an easy way is to select Editing Tools->Merge Records in GEDitCOM II while holding down the option key). In GEDitCOM Editor, expand the Scripts section and click on "Find and Merge Duplicates.py" (the first one). Scroll down to nearly the bottom to find section beginning in "if merit > 0. :" (easy way is to use Find command and search for "if merit > 0"). 11 lines before that line is a line beginning in "choice = GetOption(...". Replace that line with the code above. This will prompt you only if merit is below the number you enter (above is 95). If equal or above that score, the merge will happen without prompting. If you are not used to Python programming, it is very finicky about indents. I tried to give correct indents in above snippet. When done, the above "if" and "else" lines should be indented same as line above it while the two choice lines should be indented 4 spaces.
Merging is a challenging topic. You can try different cutoffs and check the results. If you are getting GEDCOMs from other sources, this script is be best hope for semi-automating merging. If all files were created in GEDitCOM II, you may be able to do automatic merging with no prompts by using UUIDs. The help explains how to use UUIDs and importantly what is needed for that method to be available.
John Nairn