Welcome to the forum.
I don't think that you have a frame issue. You have the correct center stand and if you adjust the bolt you see in the middle of the top part then you can lower the position when the stand is up.
Check the rear tire size, stock is a 3.50 x 18 tire, if it is a larger width then it will have a taller sidewall and give you the issue you describe. The other possibility is someone installed longer than stock rear shocks.
I did have one bike that had been transported with the stand down while being strapped on a trailer on several trips. The frame was pounded in and I had to weld patches in plus straighten out the pivot area.