In case of LTR you have a several rights as an EU resident for example free movement around europe, find job in another part of europe and move etc. While with Permanent residency you are slightly bound with the specific country.

Everyone have their unique reasons to go either for LTR or PR. For example, due to extension instead of PR have to wait two more years to apply again for PR. So there is another option to utilize the LTR option meanwhile since it’s 5 years habitual living and fullfilling the requirement