Although I am not an expert for setting up a SIB trailer, I can tell you mine is set up differently. The bunks are horizontal and mounted completely under the transom, not under the tubes. I would say it should be one or the other, but not both and especially at an angle. They are pretty tough little boats though and it probably won't damage it at all. The bunks sticking out the back looks good and about the same as mine. My boat also rests on my fenders, when it is deflated. Once properly inflated it rises off of them. I just rebuilt my trailer bunk stanchions, and could have easily raised it higher, but I choose not to in order to make launch and recovery easier since the trailer does not have to go as deep in the water.
The bow roller on mine sits lower and comes out under the bow handle. Therefore I do run my winch
(If I ever called my woman a wench...oh boy) strap over the bow roller. Both my rollers are also flatter allowing a larger contact area. I do clip the winch line off to the bow handle *shrugs*, but I won't anchor my boat that way, and instead anchor it off the d-rings along the sides run through the front handle.
You already said you have them, but I am a firm believer in transom tie downs. After watching my Nautique bounce off the trailer when I was only towing it a mile, I vowed to never do it again.
I would highly recommend checking your trailer lug nuts within 50 miles or less of home. They do come loose and it is better to take a few minutes and check them, then wind up with a problem. A spare tire is a must have with single axle trailers, and if put forward on the tongue would add some weight too. Make sure your jack and lug wrench fit the trailer.
Have fun! and looking forward to your outing report