Yes, there is a little difference.
I was doing calcs for the post of counter the mon, which now is Thundurus-T, because I am not going to post any counter, I consider interesant show them here:
The calcs are using Timid, not Modest.
Gastrodon 252 HP / 252 Sp Def +Sp Def against Thundurus-T +Sp 252 Sp Att:
Focus Blast: 27%-32%
Ice Beam: 51%-60%
Scald: 32%-38%
Most important, Gastrodon with EQ and non hindering attack nature deals a 26% to 252 HP Keldeo, thus, always breaks its Substitutes.
Keldeo with 0 HP, 31%-38%
Keldeo does to Gastrodon with Secret Sword: 44%-53% supposing 252 Sp Att Ev's of the pony and non Sp Att boosting nature.
Also, I have found the best counter to Thundurus-T, bar Shedinja(lol):
Gardevoir @ Leftovers
Trace
252 HP / 252 Def or 252 Sp Def / 4 Spd
- Psychic
- Will-O-Wisp
- Filler
- Filler
Thundurus-T only deals to it between 27,3% and 32,5% without a Sp Def Evs and non boosting nature, when Life Orbed when Gardevoir deals to him 50%-59%, a clear 2KO without Rocks and no-Leftovers on Thundurus-T.
With boosting nature and 252 Evs in Sp Def: 20%-26%
Ok, if Thundurus-T uses Nasty Plot on the switch, and if Gardevoir has no Sp Def Ev's and not-boostering nature, Gardevoir will die, but Thundurus will be around 30% of health due to 2 Life Orb damage and Psychic damage.
WoW is almost needed for to damage those annoying Scizor and Tyranitar trying to pursue it and Psychic is necessary for "reliable" STAB and a way for to hit things. WoW isn't much expected on this thing.
The two slots are very customizable, because Gardevoir has a huge supporting movepool. Taunt avoids hazards, recovers and slow set-uppers, Wish/Pain Split for healing(sadly, Wish is almost needed with Protect which is annoying in a Pokemon which suffers a 4MSS)
Heal Bell to clean status, specially on Stall Teams, Reflect/Light Screen, Toxic, Torment+Protect(used against CB Scizor on the switch and force it out) HP Fire, HP Ice, Focus Blast for Heatran and Tyranitar, the underrated Healing Wish, Charm, Thunder Wave...
The main problem is trying it to work in the metagame. It sounds great in paper, but...(I haven't tested it yet) Trapping Pursuit users would be advisable(in fact, it's easy to trap them, Dug for Tyranitar and Magnezone/ton for Scizor)
Edit: I have realized that it can learn Disable, Protect+Disable for Pursuit. it looks curious.