This whole Champions/E4s only use their Ace “99% of the time” notion is faulty. The appearances of Champions/E4s in the series are: Lorelei, Bruno, Lance, Steven, Drake, Agatha, Lucian, Aaron, Flint, Bertha, Cynthia, Caitlin, Alder, Diantha, Siebold, Malva, Wikstrom.
Lorelei: Used non-Ace Pokémon, Bruno: Didn’t use any Pokémon, Lance: Used non-Ace Pokémon, Steven: Used non-Ace Pokémon, Drake: Used non-Ace Pokémon, Agatha: Used non-Ace Pokémon, Lucian: Only Used Ace Pokemon (though he did use Giraferig on-screen in the “champion league finale” re-run), Aaron: Used non-Ace Pokémon, Flint: Only Used Ace Pokémon, Bertha: Used non-Ace Pokémon, Cynthia: Used non-Ace Pokémon, Alder: Only Used Ace Pokémon, Caitlin: Only Used Ace Pokémon, Diantha: Only Used Ace Pokémon, Malva: Only Used Ace Pokémon, Siebold: Only Used Ace Pokémon, Wikstrom: Only Used Ace Pokemon. Therefore, more often than not E4 and Champion Pokémon did showcase their non-Aces. And if you’re going to say that the pattern was a shift towards only using Aces for later gen E4s and Champions then that still doesn’t explain why Steven didn’t use any of his other Pokémon when we know for a fact that he has a very powerful Aggron. If you’re going to say that no E4/Champion shower any non-Ace Pokémon post-DP then then that’d be incorrect since Cynthia showcased that she had a Glaceon in BW and also Steven’s Aaron makes a cameo appearance in ME Act 2. Regardless of what any of these perceived patterns the following are still objective facts:
— Malva, Diantha and Steven had 5 other first rate Pokémon by definition
— Malva, Diantha and Steven used none of those other Pokémon during the TF climax
— No other characters barring Ash, Serena, and Clemont (a.k.a the main characters) were shown using non-Ace Pokémon in the TF climax
— Alain must be proficient at catching Pokémon because he was able to give Marin solid advice on the matter
— Alain had been traveling on his journey for a long time and hence was already an expereinced trainer when we first saw him
All of this would indicate that all the Pokémon Alain used at the league were indeed his and that he most likely caught them sometime during his journey as a trainer. Your claims:
Claim 1: Alain didn’t utilize his other 5 Pokémon while Lysandre and Ash used all the Pokémon at their disposal, hence those Pokémon weren’t his since he didn’t use them when supposedly trying his hardest against Lysandre.
Problem with this claim: If it was truly the case that some of Alain’s Pokémon belonged to TF, then why didn’t the anime make any explicit indication of this? Note that they didn’t need to have a character explicitly state this in order to make the indication; for example they could have just shown a 5 second scene of TF confiscating Alain’s other Pokémon (which I presume is what you think they did hence why you believe Alain didn’t have those other Pokémon at the time). The 2nd issue is that like it or not there are plausible explanations for why Alain didn’t use his other Pokémon (e.g. space constraints, wanted to focus his attention solely on Charizard etc..). Now we can argue all day about the likelihood of these reasons being the case but the facts are that:
A) Our default expectation is that those Pokémon were indeed Alain’s
B) There are plausible explanations (a.k.a those with non-trivial probability) which explain why Alain didn’t use his other Pokémon
Therefore, the burden of proof is on you to provide definitive evidence in support of those Pokémon not being Alain’s.
Claim 2: Alain didn’t use any of his other Pokémon during the Primals crisis in ME Act 3, therefore he didn’t have any other Pokémon at the time.
Well the first issue is that again Steven was also their yet we don’t see the guy send out his Aggron. Also once again we do have a plausible explanation for why Alain and Steven didn’t send out their other Pokémon which is that they would’ve stood no chance against the Primals due to such a massive disparity in battle viability. Finally even if Alain didn’t have any other Pokémon at the time, there’s always the possibility that he caught them between then and the Kalos League. On a side note his other Pokémon weren’t seen during the ME specials in general since by their very nature the focus was on ME Pokémon in those specials and Alain’s goal in them solely revolved around Charizard.
Finally excluding Charizard Alain does show visible concern for some of his Pokémon during the KL finals namely Metagross and Bisharp which drastically reduces the probability even further that those 2 weren’t Alain’s Pokémon. Of particular interest is Bisharp since he would be a prime TF Pokémon candidate (if there were any) and would’ve been 1 of the best options to use in the situation against Lysandre (if Alain were to use any of his non-Aces) due to it being relatively small and nimble as you put it though both Alain’s explicit worry for Bisharp when it got hit by Bide as well as him spurring Bisharp on when it was about to fight Greninja go against the notion that Bisharp was a “borrowed” Pokémon since from what we’ve seen Alain did have a fairly strong bond with Bisharp (he also did with Metagross though you’ve already accepted that Metagross most likely wasn’t borrowed especially since we saw it in XYZ 23 and Alain acknowledged it as his Pokémon).
In conclusion based on the evidence presented in the series I don’t think it is reasonable to conclude that some of Alain’s Pokémon were given to him by TF.