The following is taken from Frank Manuel, The Religion of Isaac Newton, 135-36. It is a direct quote from Newton. I think it shows that Newton believed that Christ would come invisibly at his second coming. Although no one to my knowledge went into the meaning of parousia until the nineteenth century, it seems very evident that the idea of the invisible coming or presence was not that uncommon in the seventeenth and eighteenth centuries. I've found other references.

"... we are not to conceive that Christ and the Children of the resurrection shall reign over [mortals] the nations after the manner of mortal Kings or convers with mortals as mortals do with one another; but rather as Christ after his resurrection continued for some time on earth invisible to mortals unless [when] upon certain occasions when he thought fit to appear to [mortals] his disciples; so it is to be conceived that at his second coming he and the children of the resurrection shall reign invisibly unless they shall think fit upon any extraordinary occasions to appear. And as Christ after some stay in or neare the regions of this earth ascended into heaven so after the resurrection of the dead it may be in their power [also] to leave this earth at pleasure and accompany him into any part of the heavens, that no region in the whole Univers may want its inhabitants."

Jim