The benefit of the feat Improvisation says, in part, "You gain a +2 bonus on all skill checks for skills you have no ranks in." The description of the extraordinary ability master armorer, an advanced armor training ability, says, in part, "The fighter substitutes his total base attack bonus… for his ranks in [the Craft (armor)] skill…."
This reader believes that this combination should be read as follows: The fighter that possesses the ability master craftsman simultaneously loses any actual ranks in the skill Craft (armor) and gains a number of effective ranks in the skill Craft (armor) equal to the fighter's base attack bonus. Thus the fighter would have ranks (albeit ersatz ranks) in the skill Craft (armor), and the bonus from the feat Improvisation wouldn't apply.
(Keep in mind that the skill Craft (armor) is typically a fighter class skill and "[i]f the skill you’re using is a class skill (and you have invested ranks into that skill), you gain a +3 bonus on the check" (see here on Class Skills). These effective ranks should satisfy this requirement (and would in this GM's campaign), making it so the previously-0-ranks-in-Craft (armor) fighter may receive that +3 bonus, bettering the bonus lost from not being able to apply the Improvisation feat!)
The alternative is to read this combination as the fighter that possesses the ability master craftsman simultaneously losing any actual ranks in the skill Craft (armor) and gaining an untyped bonus to her Craft (armor) skill checks equal to her base attack bonus. While this would result in a further bonus from the feat Improvisation, the description of the master craftsman ability doesn't actually say that… but the master craftsman ability also does not say what truly happens to the fighter's base attack bonus when it's substituted for her ranks in the Craft (armor) skill. However, that explanation would be tough sell to this GM: The game tends to rely on specific exceptions and says what happens when exceptions are made, and there's just nothing about untyped bonuses and stuff here. You can ask your own GM if he'll read this combination this way, but it's not a reading I'd stake my PC's life on. To this reader, that seems too risky an intuitive leap.
Note: This answer addresses this issue solely from a rules perspective. On a more practical level, this GM just doesn't see a problem with the feat Improvisation granting a fighter that possesses the ability master craftsman another +2 bonus on her Craft (armor) skill checks. That's a really small bonus—so small as to likely not matter at all in the grand scheme of the campaign.