Asterisk hasn’t had a web GUI that was supported in this forum for at least the best part of a decade. The only GUI that has any reasonable level of support is the one you say you are using, and peer support for that is provided at https://community.freepbx.org/
I’d note that FreePBX uses “extension” differently from Asterisk, using it for both the things defined in extensions.conf and those defined, in your case, in sip.conf, whose names it aligns. The only thing I can think of which might make a configuration reload, on Asterisk itself, slow, is if you have static hosts in sip.conf and one of your DNS servers is timing out.
(As others are hinting, FreePBX completely rewrites various configuration files during an update, and it is possible that you have a file that is so large that the time to do this is becoming significant. Bare Asterisk users would, typically, use Asterisk Realtime Architecture, if they had to manage huge numbers of changing “extensions”.)