I think it’s so close they didn’t want to take the risk? Assuming the voting intentions between Letwin amendment and government’s deal are similar, they would need another 10 votes for the deal to pass, from labour rebels/the handful of abstainees. They’ll be harder to convince by the hour, as more time spent scrutinising the deal will expose its faults.
The government’s repeated shouting about how there are enough numbers feels to me, like they’re putting a brave face on it. They’re trying to make it look like it’s the remoaners/parliament that are blocking the tories, and if those groups stopped playing dirty eased off this would easily go through. It’s a better narrative than “It might get through but we’re a weak government and it’s too close to call?”
That said I’m not 100% why the government even attempted to have the vote yesterday, unless they never expected to have it and wanted to drum up greater anti-parliament sentiment.