Even if you apply online you need to actually be in Taiwan to apply there... you need to visit the National Immigration Agency to get this certificate and submit it to the embassy as requested (this is to prove that you are IN the country where you apply).
did you do a 30 day extension already? If not, then do that in Krabi instead of a border bounce. I've never seen any long ques at the The immigration office in Krabi, it's 1900 thb and quickly done. If you have an extension already, flying from Krabi to Kuala Lumpur and return is the most convenient.
Even though we know that some people have been approved with 1 month activities, we also know that others have been rejected with 1 month activities... This varies among the embassies/consulates so it is advisable to research the requirements of the embassy where you plan to apply. It is best to read all information provided on the specific embassys webpage plus using the search function in this group to read application-reports from that city.
If you can find a solution where you plan to spend most of your time (Phangan?) that is the best, since that will allow ATM-withdrawls inside the province without any fee.