Toran Frostbite
Highrise Above All
It's a question of relation. Generally, you assume if both or all the pokémon involved are owned by relatable to the groups they're involved in, the 'ship means the specific characters.And a couple questions:
Is there a difference between, say, Treecko x Totodile vs. Ash's Treecko x Ash's Totodile? I'm certain it's been asked before, but I've never really found an answer...
Is there any particular convention for choosing between two more or less equally used names? (probably not, but...)
Any pokémon owned currently, in his team or Oak'd, involved in a 'ship are generally considered specific ownership first, random critters later. You say Piplup/Pikachu, you think Dawn's and Ash's, because of the group they're in, even if they aren't identified. Likely, that's who they'll mean anyway.
Any of TR's pokémon mixing among their associated partners (Weezing/Arbok) are easily constrewn, and 'ships like Weezing/Yanmega may or may not need James' and Jessie's tags, because they never associated during the same timetable. However, Weezing/Mime Jr wouldn't, because bth are owned by James and share that instant insight to ownership.
Zoey's Glameow and Kenny's Breloom would need tags, because while they are coomonly associated as Coordinators, they don't travel together, like any of Ash/Dawn/Brock/etc's pokémon do. Dawn's Piplup and Misty's Psyduck would need to be tagged, because even if they do meet and hang for five episodes, they won't travel to the extent of the mainmain group of the Gen.
^^; In short: it's all about relativity. For Treecko/Totodile? It'd be Ash's first, wild second, even if it's not tagged as Ash's. If there are two separate 'ships for tagged and untagged, either assume there's a good reason, it's old and no one can replace it, or it slipped past us.
...it's probably not a decipherable answer and I'm sorry for that. =\