They weren't using them to reduce colonial autonomy any more in the 1760s than when they were originally passed.
That American propagandists tied the two together doesn't mean they had a link.
Given that its attempts to do so is exactly why we have the issues of the 1760s .. .
Yes this is my point. The fact is radical Americans won the propaganda battle and made out the taxes to be something they weren't. The Americans didn't have much of an issue about them before all the tumult of the 1760s, much of which was caused by blatant lies and rumour mongering. Quite a bit spread by people who would be economically disadvantaged by the restrain on land speculation and smuggling.
The idea that America was a great industrial nation in the making in the 1780s-1820s and would have been held back by the navigation acts if it had remained in the Empire is just wrong. It wasn't and there was no overriding desire to begin spamming out goods restricted by British trade restrictions. Jeffersonian agrarian ideals dominated and most considered Britain as the natural place to get their manufactured goods from. Industrial America didn't really begin developing until the Erie Canal and even then it was a slow burn. It was only in the 1820s when it regained it's pre-Revolutionary economic strength.
What fuelled the protest against British taxes was economic recession and the propaganised belief that parliament was using it's taxes to break America's autonomy, whereas in the past parliamentary taxes had always been half assed and designed for imperial preference rather than all these wild rumours about tyranny and repression.
If they'd cracked down on rum in the 1740s no large scale protests would have broke out. By the time they did in the 1760s (after the Tea Party) it had become part of a greater narrative, a narrative that made it appear like parliament was trying to remove the colonies autonomy rather than just regulate trade.
A modern example. I'm not particularly arsed that the EU costs me money by running the CAP and subsiding French farmers and making me buy their produce. Of course it annoys me but I'm not fuming about it. However if the EU introduced new taxes, installed an army in my town, economic recession was raging and everyone around me told me that the taxes and army were there not for my defence but to put the EU in charge and reduce my autonomy, I'd become mightily suspicious and militant. Both times I'm paying taxes but my attitude to them has changed greatly because of the supposed situation at hand.
So I don't particularly believe that continuing to enforce a form of the navigation acts and retarding American industrial progress would be an issue between Britain and America. So long as an accord was reached between the two as it had been up until 1763, however it required better more efficient politicians than the type Britain had at the time. Also if America had remained in the Empire, free trade currents would have reached Britain before 1840 (otl) and in the absence of an Imperial parliament, Dominion status would be becoming a more debated subject in America as it's industrial take off begins.