That's unlikely, so you're correct in parsing it as a statement being made, not than something that they actually -want- to have happen.
This is extremely common in the US congress.
There are two things missing:
1. Congress can override a Presidential veto with a vote a two-thirds majority in the both chambers.
2. The President can also let a Bill sit for 11 or 12 days (it's really 10, but Sundays don't count.) At that point it becomes law without the President's signature.
2. The President can also let a Bill sit for 11 or 12 days (it's really 10, but Sundays don't count.) At that point it becomes law without the President's signature UNLESS CONGRESS ADJORNS DURING THIS PERIOD, THEN IT DOES NOT BECOME LAW (KNOWN AS A "POCKET VETO").
https://news.ycombinator.com/item?id=6098357
Yes he could veto the bill, but this bill contains multiple parts and I believe is the entire DoD budget. So if he did so the US would have no DoD budget. That would be very bad for him.
None of the other comments here are wrong, but they don't address the issue of a Presidential Veto affecting the entire bill not just the amendment.