With hindsight, it would've been better staying under Tramiel's Atari company, away from the Goulds and the Alis. Although Sam Tramiel would've sunk it in the end anyway. There was really no stopping PC sales. Modularity. Ah well, too late now anyway.
It would have never been under his company. What you have is a chain of events: 1) Jack announced buying Atari's Consumer Division to form Atari Corporation almost simultanious to Commodore announcing they're buying Amiga. 2) Commodore immediately sues Shiraz and two others of Jack's engineering staff for theft of trade secrets and puts an injunction on them doing any computer work for Jack that lasts through the entire month. 3) Jack's son Leonard discovers the cancelled check from the previous Atari's investment in Amiga. Jack contacts Warner about it, negotiates for the contract with Amiga (it was with Warner but executed through it's Atari subsidiary) and launches a countersuit at Commodore via Amiga. 4) Both suits are settled out of court.
Without Commodore buying Amiga, you simply have a lawsuit against Shiraz and the two others and Jack with no way to apply leverage to fight it. Amiga would have been out of the equation. Likewise, the contract with the original Atari Inc. that Jack was suing over was never for any sort of ownership. It was simply for licensing (which Amiga would have made a ton of money from under the terms) and access to the chip documentation being held in escrow should Amiga go under. Amiga had several investors besides Atari, and Atari needed a way to recover their investment. If Amiga went under because of their financial problems, Atari Inc. would recieve the right to manufacture the chips on their own, no licensing required.
Regardless, had Commodore not bought it Amiga would have simply soldiered on seeking more investors and a potential buyout, or gone under because of the bad financial state they were in and its assets split up among the investors.