There is a mismatch if the player decide that has to be.
All the companions backgrounds, once you start discovering their story, plenty justify the fact that they are at level one. Not to forget that a level one is however above the average sentient being in Faerun.
As I said before: Gale as messed up the weave and lost his connection with Mystral, he has done so much damage that being alive and at level one is a better outcome in comparison of what he could have got (nevertheless he still is in danger of explode); Will tried to take a step back from his contract with his patron, patron that has been kidnapped thus weakening his connection to the source of his powers; Astarion is not a full fledged vampire, he is a minion, a slave that Cazador used as entertainment fo lash out his sadistic aspects; Laez'el is a low rank gith; Shadowheart was sent in a mission that required her memory to be erased.
So how is it incoherent the fact that they are at level one?
About the supposed contradiction between the introductive cut scene and the subsequent fights. The vessel was a transport for kidnapped and infested beings, a ship that strays from its course and ends up in hell, then it crashes in a very casual place, so casual that it is at the center of a conspiracy that sees bugbears, drows, goblins allied, with the gobbos betraying their faith to follow a new cult, in this place the darkdruids are making their move, the hag has contacts and does affairs with people in Baldur's Gate, meanwhile the party find people like Volo (a comic relief but still a personality of note in Faerun), can make alliance with Hasrim (an arch druid) or Minthara, you have to interact with the Flaming Fist, the Zentharim.
All in the introduction.
As far as I can see there's a lot of coherence with the background of the companions (and in my case even too complex stuff for my freshly "graduated" Tav fighter), who were person of some social impact and find them selves in the middle of a conspiracy of such level that a demon of high level like Raphael decides to gave them a visit.
But again, if a players decides that there's an incoherence than incoherence there is.
Arcane magic does not mean the god has to grant you spells like with divine magic. If Gale can use the weave at all he would have access to all his normal spells. He would only lose chosen abilities like silver fire. Not to mention all the knowledge he would have.
Astarion is still a vampire spawn, meaning a monster with regeneration, claw and bite attacks, 80 HP, etc. And as it was already mentioned. Arch druids are a title you get at level 14.