Gun permits (what they were called in the 70s and before) are state licenses to avoid the reciprocity problems of 67 counties honoring each others license (or not).
Licensing was undertaken with the base line of need. Reason for applying questions were part of the application.

In other words, the attitude has historically been arming a citizen is a dangerous proposition, proceed with caution. It took a while, and probably some legal challenges, to advance from "show need" to "will issue".

County sheriffs act for the needs of the commonwealth. They were saddled with it by how the licensing was designed. With 67 sheriffs participating, there's going to be 67 different personalities (and beliefs) tugging at how it is administered. There is going to be 67 views of where in the tiers of responsibility LTCF resides in their office. It is unfortunate that on the clerk level, the clerk's attitudes enhance or taint the process.

Good question re state license, why only county of residence? Sheriff has no interest and actually no standing with respect to anyone in another county wanting any kind of license. He does have interest and standing in residents of his/her county. And since there is a charge, they may have no way of charging the resident of another county.

Like I said, gun permit applicants have been historically viewed negatively in a may issue atmosphere. May issue was an exclusive membership, such as NYC licensees are today.