My take and experience on this. I just did this for the first time at 49K miles. No issues with the transmission to note before doing this. While looking at the bottom of the transmission while the car was up on ramps for an oil change, the first thing I saw from below is the filler bolt on the side of the transmission is tucked up in a hole surrounded by the sub frame. The bolt hole has a good chance of making a mess in the whole area and the only real access is from the wheel well, with the tire off. You could probably work on it underneath using the room around the tire and the wheel well to take the bolt off and re-torque but it seemed to much of a PITA without taking off the wheel. That leaves putting the car on a couple of stands in the front and then jacking up the rear to get it level and either holding there with the jack or a couple of more stands at the rear points. I'm only going to be underneath the front of the car at the time, so the stands will hold the front up in the event the jack takes a squat while holding up the rear end.
So I took a look from the topside to see how bad it is to use the upper fill bolt as the OP suggests. It's underneath the stock air box so you need to remove it to get good access to it (unless you have a non-stock option like the OP did and removal is not necessary). Removing the box is easy. Disconnect the MAF sensor on the top of the box and disconnect the snorkel hose. Remove the top and filter completely and set aside. Remove the single 10mm bolt in the front right and then pull the rear of the box up and free it from two aluminum studs. The rear of the box fits on the studs with rubber grommets. Just ease it off and don't jerk it up into the master cylinder. Now you will have a clear view of the filler bolt. Crack it open and leave in place to keep out any crap.
Go below and prep for the drain. Keep in mind the car is still only on front ramps with tires, the rear is still on the ground. Get a piece of aluminum foil, around 2 ft long and cover the subframe right beside the drain. Let half of it hang below the subframe and form it to angle the drain flow into a bucket. The foil keeps the mess at a minimum but mainly directs the flow into a bucket. Crack open the drain bolt and remove. It will come out slowly at first until you fully remove the top filler bolt to allow it to vent. Remove the top bolt and let it all dump into the bucket. Once empty, reinstall and torque the drain bolt. Keep in mind, I am not touching the side filler bolt, it remains installed. Remove the foil and everything is clean.
The bucket I used has volume markings so I observed 2 full quarts came out of the transmission. Right on the dot, two quarts. The fluid was translucent when it was draining out and I didn't find any crap or metal in the bottom of the bucket when draining it out. Draining the car at an angle has no issues.
So with 2 full quarts drained, I filled through the top with 2 full quarts of new MTF. No mess. No squeezing a bottle, pumping a pump or feeding through a funnel with a j pipe on the end to fill through the side. I put back in exactly what I took out and it agrees with the amount shown in the manual. Reinstall and torque the top fill bolt and reinstall the air box. Done, easy and no mess.
Another cool thing removing the top fill bolt allows you a peek inside the tranny. Everything looked new and clean. If you have one of those snake inspection cameras, you could see more.