As far as I'm aware, WHM's and AST's lore are still consistent/intact.
They may have changed mechanically, but they still retain (most) of their toolkits as they were presented within their respective stories.
Also, about them "not caring about the lore" is a flat-out lie.
Else they wouldn't have justified them with supplemental material such as encyclopaedia entries or "Tales of" stories.
Every single class/job in the game develops from the foundations they started with.
"Summoner" is an Allagan discipline specifically designed to counter Primals by using their own powers/essences against them.
And Egis are just as essential to them as faeries are for Scholar or cards are for Astrologian.
They may add new toys such as Trances/Demi-Summons or what-have-you. But Egis are not going away.
That's a slippery slope.
If people wanted to change the story/lore because they "don't like it", then where would that lead us? and where would that end?
Classes/jobs' stories/lore are just as important to this game's universe as the MSQ.
In any case, them "reworking" both Bard and Machinist is proof that they can change a job mechanically while also keep its story and identity intact.
And I expect the same out of Summoner in the near future (while keeping Egis around).