I have been having the exact same issue with my 2016 2.8 SR5 hilux. It started at around 280km. I now have 14000km one year later and numerous trips back to the dealer and they said they can't reproduce it. One instance we did reproduce it and the test driver said it's normal.
This is in addition to, a squeak in the rear right still not resolved, voice activation taking upto 1 minute to respond, navigator restarting a few times on its own, whining noise coming from engine when cold in mornings.
I know its not normal, because I have driven other Hiluxes like mine and they don't flare or ***** between gear changes.
My symptoms are the same, however from cold, when i accelerate, between 2nd-3rd or 3rd-4th and 4th-5th, sometimes it flares, and sometimes it feels like someone bumped me from the back, either way, the car feels like it pulls back before engaging the next gear.
If I try to over take on the highway, at around 70kms/hr, and I accelerate, it is indecisive as to which gear to engage at first.
So far, I have taken it to my purchasing Dealer throughout the year, and two other dealers to see if they can see what the issue is. Each time, they didn't check the oil levels.
At least I know I'm not the only one experiencing this problem as my dealer is suggesting it is all in my head.