As long as a customs union provision wasn’t drafted so as to preclude ratification of the withdrawal agreement (for example like this) Johnson could accept it, ratify the WA, secure Brexit, and then hope to repeal it in a new Parliament after the election we all expect soon. 
As I said yesterday, such things are written on water: they can be repealed by the next Act of Parliament. Nor does it matter in terms of ratification that such a provision would at some stage require a change to the political declaration: that is not binding hard law.
(The photo is of a provision inserted by the Lords into last session’s Trade Bill.)
The only CU amendment that would prevent ratification is one that required change to the WA now.
For example, one that provided that the Government may not ratify the WA unless it contains provision for an all-UK/EU CU in the event that no alternative free trade agreement is agreed at the end of the transition period.
(We know such a thing can be agreed as it was in the May agreement.)
The difference between these two types of customs union amendment is very important.
It is only the second type that binds a new government after an election: it would require a backstop CU agreement to be created as a matter of international law. And it is only the second type that would prevent ratification of the WA now.
This is a good point.
But it wouldn’t stop ratification. And it would still be written on water.
Johnson could almost certainly get the required amendment to the political declaration (explaining it was need to get ratification) while explaining that he would revisit it after an election.
And after he won an election, he would repeal the offending provision and go back to the EU asking for the current NI-only PD again.
