The answer to this very important question about what sort of amendment would stop the Bill and prevent ratification of the WA and thus Brexit with this deal is that you have to distinguish two cases.
The first case is a real poison pill: an amendment that would stop Govt from ratifying the WA. Examples: an amendment that required a referendum before ratification or, from the other end, one that stripped away the required supremacy of EU law for transition.
The first would on its face stop ratification: the second would do so in practice because the UK would be in immediate breach of the WA once ratified.
The second case is an amendment that really bites only after transition: eg an amendment requiring the Govt to negotiate a customs union/common market 2.0 or enshrined commitments to workers’ rights/ environmental protection.
Such amendments would not prevent ratification, as they are entirely consistent with the WA. They would impact the political declaration: but that is aspiration, not hard law.
In the face of such amendments, Johnson could properly accept them, proceed with the Bill and ratify the WA.
He could then call (ie propose, with likely Labour support) a post-Brexit general election, in which he could promise to repeal the disliked amendments. And then carry out that promise if given a sufficient majority.
Important point for those accepting the deal and relying on amendments to take off the hard edges: such amendments are written on water, as what is in one Act of Parliament can easily be repealed by another.
NB - the way of turning a “Customs Union” amendment into a poison pill that would prevent ratification would be to go beyond this ... 
... and to prohibit the Govt from ratifying the WA unless it is amended so as to contain an all-UK customs union backstop.
