No, not as standalone words. bon is pronounced with a slightly nasalised "o", and you don't hear the "n" apart from the nasalisation. bonne has a cleaner "o", with a distinct "n" at the end.
If bon is followed by a word starting with a vowel sound, you liase the "n" onto the following vowel, and it sounds much more like bonne.
I think "Le bon pain" means that "good" is an inherent and inseparable quality of the bread, making it a definitive description, e.g. "I would like the small sandwich- it has the good bread."
"Le pain est bon" is describing a specific bread, but not identifying which bread based on the fact that it is 'good.' "I would like the large sandwich- the bread is good.'
While you can say it that way, they are not equivalent. "Le bon pain" means "the good bread" : an incomplete sentence ('The good bread is in the shopping bag', for example). "Le pain est bon" means "the bread is good" : a complete sentence. The difference between the two in English also exists in French.