As far as lightsaber stabbing goes.. Cal Kestis survived a stabbing too.
The big thing everyone keeps ignoring when they complain about it is location..
Sabine was through the lower right side of the chest, right through the liver and upper large intestine. With cauterization, survivable long enough to get to medical care. Which she got immediately, with ahsoka having medical stuff on her ship and then flying sabine to the hospital.
Qui gon jinn was stabbed just under the sternum, angled upwards. Right into the heart. It would have flash boiled the blood in the lower chambers and literally exploded it. That he lasted long enough to get out a few last words was practically a miracle.
So not a plothole.
As for the prison ship captain.. yeah the guy was arrogant and could have handled things better, but given there is a new jedi order in the new republic, i suspect he though the potential for them to be actual pre-imperial jedi now coming out of hiding warranted investigation. His biggest flaw was he underestimated the capability of the people who came aboard.. but few people even before the empire knew how dangerous a jedi could be, and the captain clearly thought he was dealing with some imperial officers in cosplay, not actual force users
And the star map gets some context in ep2.. its not to Thrawn specifically, but a map of routes between the local galaxies, and the dathomir lady has had visions that one of those galaxies is where thrawn ended up.
Personally i find the ship she's building for the trip interesting.. its a giant hyperspace ring, like was used for fighters in the clone wars. At first i didn't know why she'd do a ring much less one that scale, but then it occured ro me.. Thrawn didn't dissappear alone. He vanished alongside the entire Seventh Fleet, a force of at least 31 star destroyers, a dozen of Arquitens-class cruisers and gozanti patrol cruisers, amd at least four dreadnought heavy cruisers. (Per wookieepedia). And hyperdrive rings are used to carry smaller vessels through hyperspace. She's building a supership nthat can haul back a substantial portion of Thrawn's former fleet once they've found him.
[./spoiler].