It will mix just fine, sitting there. I would NOT drive it around. The pumps will circulate the hydraulic oil at the rate of about 6-7 gallons per minute. I would be surprised if you need to even run it for that long to see the dye show up in the glass...
So you most likely will need to drain out (suck out) that 3 gallons you added.
I run my hydraulics with a extra gallon because there was a Product Improvement Bulletin where the early models of these "Standard" L's with ratching CAMS had their oil level elevated by 1.?? (something) gallons to submerge the CAMS in oil. That was Kubota engineers that came up with that solution. The sight glass was replaced with a dip stick to measure the higher level.
I don't think running extra oil is a problem - the size of the oil sump/tank is mainly to deal with cooling the oil. I lost 3 gallons and were still able to drive the tractor back to the house, with no problem.