I've seen that pencil factory foundation... I think you'll find I'm of like mind on the origin and use - and re-use - question. But I believe we can know more than you think. However, ignoring dating that shows they were built prior to colonization seems unscientific when one is building a hypothesis. And the walls are not simply from colonial field clearing, as has also been shown through dating. In New England especially, the land has been churned by settlement, but there is evidence the walls and stone structures are older, and likely indigenous.
As for the bridge arch, no it's not on old maps, this is just a culvert. Maps, gazeteers, town histories - this site was pretty thoroughly researched by myself and Joe, I simply cannot share too much because of keeping the location secret.
If interested, check out the book Stone Prayers I cite in the article, quality recent scholarship.