Have you been in the deep south? or just read stupid stuff on it, I am over there 5 times per year and never encountered any problems, maybe a good thing is more talking negatively about it and less foreigners so us we can enjoy 100 times more
You have more chance to die from a motorbike accident in Phuket than getting in trouble in the south, dont listen to the negative comments from people who never been in the deep south, Betong area is fantastic
No forget about applying outside of Thailand they will give you only 90 days with all company documents and work permit letter. so better do it in Thailand