For the benefit of anyone having the same question:
After consulting with the git config documentation, I came to the conclusion that this config change should only be run once, using the same git.exe path that is configured in Jenkins:
"C:\Program Files (x86)\Git\bin\git.exe" config --system core.longpaths true
This can be later verified by listing the various settings:
"C:\Program Files (x86)\Git\bin\git.exe" config -l
core.symlinks=false
core.autocrlf=true
core.longpaths=true
color.diff=auto
color.status=auto
color.branch=auto
color.interactive=true
pack.packsizelimit=2g
help.format=html
http.sslcainfo=/bin/curl-ca-bundle.crt
sendemail.smtpserver=/bin/msmtp.exe
diff.astextplain.textconv=astextplain
rebase.autosquash=true
merge.tool=kdiff3
mergetool.kdiff3.path=C:/Program Files (x86)/KDiff3/kdiff3.exe
diff.guitool=kdiff3
difftool.kdiff3.path=C:/Program Files (x86)/KDiff3/kdiff3.exe
core.editor="C:/Program Files (x86)/GitExtensions/GitExtensions.exe" fileeditor
There may be other ways, but I only tried this one.