"All men equal" included deportation based on race
The author of the "all men created equal clause" clarified it himself.
Jefferson's understanding of "all men equal" still included deporting all the blacks (as God also created everyone segregated in the "bounds of their habitation").
In Thomas Jefferson's Virginia Notes, he commented on his amendment to his original ordinance to deport all blacks out of America, which he submitted and said bill was reviewed in 1796.
He stated:
"The principles of the amendment however were agreed on, that is to say, the freedom of all born after a certain day, and deportation at a proper age. But it was found that the public mind would not yet bear the proposition, nor will it bear it even at this day. Yet the day is not distant when it must bear and adopt it, or worse will follow.
Nothing is more certainly written in the book of fate than that these people are to be free. Nor is it less certain that the two races, equally free, cannot live in the same government. Nature, habit, opinion has drawn indelible lines of distinction between them. It is still in our power to direct the process of emancipation and deportation peaceably and in such slow degree as that the evil will wear off insensibly, and their place be pari passu filled up by free white laborers. If, on the contrary, it is left to force itself on, human nature must shudder at the prospect." (as also found on page 91 of Mayo's "Jefferson Himself" and others quoting his "Virginia Notes" manuscript).