If you're missing deadlines, you can't both complain a) when there's no accountability and the business is going poorly, and b) when your managers are trying to hold you accountable.
Ultimately your employer has to make money to pay you for your work. Keeping this in mind is one way to help you avoid yak-shaving, bike-shedding, and other weed-entering activities.
Of course it must be coupled with genuine flexibility to change your mind when someone points out actual, real difficulties.
But he is an engineer, more so than most managers. He would know what goes into making an application like this, and so know that things are moving slower than they should.
I see nothing obnoxious about asking this very valid question under those circumstances.