Saw the source that mentions him as a scout (snippet below) but no luck on Manassas or not. Yes, he could have traveled from there since the battle (the article was published on August 23, 1861).
Checked "The Battle Flags of the Confederate Army of Tennesse" by Madaus and Needham but it only described the 1st LA Cav. flag that was captured on March 25, 1865.

"The high reputation for good judgment, coolness, and bravery acquired by Mr. S [John Scott] in Virginia, as an independant scout gives assurance that he will distinguish himself as the leader of a regiment. Caddo Gazette"
Daily Delta (New Orleans) August 23, 1861, Vol. XVI, No. 223, Page 1, Column 5

I can tell you that both Scott and Benjamin Lewis Hodge were authorized by the Secretary of War at the same time to raise a regiment of cavalry. Hodge opted out and raised a regiment of infantry instead.