Like I said, do what you have to do. Those recommendations are primarily for draft/flow considerations from what I can tell. If the stove is not lazy acting and has good draft you are likely in the clear. I agree with you, run it the way you have it for now. Your options are limited with the space you have. Here is my King Ultra with a 24" vertical section then two 45* elbows with a 12 between them to connect to my masonry thimble. About as ideal as I could get. Bottom of the thimble ends up being around 6'1".
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You can put a flexible insulated stainless steel liner down an existing chimney if there is room. Yours being 6x9 is not going to fit any insulated liner into it. A 6" linsulated liner with insulation needs about 7.5" round clearance to fit. An 8" needs 9.5" clearance. Neither are going to fit in your chimney unfortunately.
I would leave a cap off the chimney. They choke the flow slightly. The faster the flue gas can exit the less heat it will give up to the chimney and the less chance you have for creosote. Just keep an eye on your chimney. Is the best thing you can do at the moment. Burn the stove hot once or twice a day to dry out any creosote is also a good practice. If someone is home during the day to feed the stove then run the setting in high but add only 2-3 splits at a time at shorter intervals vice a full load turned down. Good luck and let us know how you make out. Give us a pic of your chimney on the exterior of you can.