No, they are not canon/connected given the raft of continuity errors within the 2016 reboot with the biggest whammy being Bliss's backstory.

Plus Craig McCracken himself wasn't involved with the reboot at all since he was still under contract with Disney at the time.

I agree, it's clear that the 2016 writers did not consider the lore points of the previous series when making their own. However, I don't think they're impossible to reconcile, if one is willing to consider the spoken word & imagery from the 1998 series and 2016 series at a purely literal level, and use some convoluted technicalities to explain facts shown in the 2016 series that seem to contradict the prior story.

For example, take the three carved windows in the Professor's house in the flashback of Bliss's story. The Movie showed us that those weren't there prior to the Girls' creation, but who said the three carvings in the flashback are the same ones? Maybe all Powerpuffs prefer window carvings arranged like that in their residence; in which case, the Professor could have had the wall filled back after Bliss's departure to repurpose the room. Like I said, it's a huge stretch, but by no means impossible.