It the same for transferring the folder/files to other location. a single 1GB file will take 5 second to transfer to external hard drive. A 1GB non-zipped folder (consists of thousands of thousand file from 1KB to 1MB each) will take half hour or more to transfer to external drive. I have a 150GB folder that contains over 500k of files, averaging 120KB to 4 MB, will take 3 hours to transfer to the external drive. I have another 120GB folder that are consist of videos, averaging 300MB to 10GB, took 20 minutes to completely transfer to external drive. This transfer through NVMe ---> spinning rust external drive through USB 3.1.
If you are pulling a large repo that have thousands of files in it will take a while for Spotlight to index each file. That is not the fault of Spotlight, that is just the way it is because it have to scan individually each file to index.