Just my opinion, but I would say the chances of it being factory are slim. I have never seen a magna-ported snubby. It could be possible, but I just don't think that was something people did to these guns often.
Someone else may know more.
That wouldn't stop me from buying it if the price was right. My 3" S&W 629 is magna-ported and I really like it. I wouldn't pay to have a gun ported, but if it was already done and I thought the price was right, I wouldn't hesitate buying one. Even a Python. I think they are fairly attractive with magna-ports, and the Python would be too. A shame though that such a desirable and expensive gun got the treatment, as I am all about factory original with Colts.
A letter will tell you for sure if it was done before shipment. If sent back, it would not say, but I don't think Colt would have taken it back and done magna-porting. I believe they had their own in house porting which was round 'dot' ports. Never know though.