The arsenal resets are done with the "ResetHealth" and "ResetInventory" lines in the mod's mapinfo's entries for the first map of each chapter, ie E2M1, E3M1, E4M1, MAP01, NV_MAP01, TN_MAP01, and PL_MAP01. So you could take those lines out for a no-reset run.
Given that I'm just using a standard mapinfo directive to do it, I'm not really sure how I'd fix mods that break it. Maybe Samsara sets certain weapons to be "never strip this item, even after a ResetInventory"? I believe the Inventory.Undroppable actor flag does this. Are those items normally stripped between Master Levels when playing without the Full Run mod?