Is it ok to sit in it on dry land?
Congratulations on your new boat!. Personally I never sit in a kayak on dry land. Some people no doubt do and may get away with it, but the bottom is not built for single point support -- it is designed to be supported over a broad surface by water in the same way airplane wings are not usually made to be stepped on but can easily support the weight of the entire plane and passengers when broadly supported by air. Cockpit rails on the other hand are designed with the rigidity to support the boat (inverted).
You would want to adjust your seat in conjunction with pedal reach while in the water when you have an opportunity to cycle the pedals. If you need to work on the rudder, you can set the boat upright on sawhorses (I pad mine) where everything is easy to inspect and access.
If the handles are not synchronized, you will not be able to adjust the rudder until you get that resolved. They are supposed to be synchronized at the factory so I'm guessing this was missed by the QA dept. I'm wondering if one of the internal lines is wrapped around something or misguided. Unfortunately it sounds like your Hobie dealer does not know how to work on his product because this is something your dealer would normally take care of for you. If you can snap a couple of pics showing the handles and internal lines someone here might be able to help. Using a mirror, you can also inspect the lines inside between the handles.
Once the handles are aligned then the rudder can be adjusted if necessary.