Do mean via HOW or BLESS? If so...

>>1. Can you make a swappable weapon a holy weapon? If so, are both weapon choices the holy weapon or just one?
Yes, it's the weapon itself not the "type" of weapon.

>>2. Can you make weapons with flares (fire, frost, etc.) a holy weapon?
Yes.

If you mean something else can you clarify please?

Rhadyn da Dwarb - Blood for fire!

Barbarian Guild Suggestions
https://docs.google.com/spreadsheets/d/1h4L5hAxR1-VLDegDNZBIhGdo5bMgnCtm84Icm2E0utU/edit#gid=0

It works with both swappable and flare weapons. I'm not sure how it is calculated, but it appears to be something more akin to the Bless or Ignite spell, and doesn't seem like it interacts with/interferes with weapon scripts such as chippers or flares in any way.

I believe it used to be more restrictive way back but was updated at some point to work with most things.

Confirmation... You can have a swappable weapon and a flare imbued weapon as your holy weapon for the Glyph of Renew quest . My friend just completed the quest and used a "Savage flamewood riste embedded with jagged blades of agonite" to complete it, charge it, and gain the bless on all versions of the weapon.

Rhadyn da Dwarb - Blood for fire!

Barbarian Guild Suggestions
https://docs.google.com/spreadsheets/d/1h4L5hAxR1-VLDegDNZBIhGdo5bMgnCtm84Icm2E0utU/edit#gid=0