95% of the bulk of the document is endless tariff elimination tables. I hope you'll forgive me that I glossed over them. If you're concerned about the ISDS mechanism the relevant parts are in Chapter 9, with some exceptions listed in Chapter 29.
Regarding the tobacco exclusions, it seems punitive to me, they were definitely being bad actors under previous ISDS mechanisms. You're right, though, the public health interest carveouts in the TPP's ISDS implementation (based on a recent Canadian BIT) would provide sufficient tools to allow unfettered regulation without needing to ban them wholesale. These carveouts were not present in the BIT in the PM vs Australia case, for example.
So why were tobacco bad actors? In the Australian case, they launched a suit claiming that by enforcing plain packaging Australia was in essence, appropriating their brand, packaging and associated goodwill. You may think they shouldn't win this argument, I may think they shouldn't win this argument, but regardless, they deserved to have their case heard fairly. They of course lost with costs.
The problem was that PM also quite likely believed that they wouldn't win, and was instead using the process to delay plain packaging legislation in other countries such as Ireland who were waiting on the case results. This would be a clear cut case of abuse, and participating in poor faith.
As per what would prevent other companies from attempting the same thing? Fear that the same thing would happen to them. Because of likely abuse of the ISDS system, tobacco would now have no international recourse whatsoever if governments flat out nationalize their factories.