you should be fine. With my job i am in Thailand for a month then leave for a month. I have been entering six times a year on visa exemptions for two years now and ive never been rejected. There is some truth in the crackdown though I suspect it's mainly aimed people constantly extending and doing border runs. There are certain things you can do to give you the best chance of not being rejected. My last 3 or 4 entries they've started paying more attention to me and have started asking to make sure I meet the requirements. These are things they've asked for, proof of a departure flight with details so I print off my flight booking confirmation, if im staying at a hotel i print off my hotel booking showing the duration of stay and hotel address and I also have 20,000 baht in cash, I keep it in foreign currency with half being USD and half being GBP. Two entries ago they asked to see all three.
ive spoken to my company to say I may need a little extra time off, I was hoping to apply for the non o here in Libya and then fly into Thailand and apply for the extension, is there a specific time during the 3 months that I can apply for the extension or could I do it on my first day in Thailand?
Like people have said its generally not doable before your last week. Just make sure a TM30 has been done for everyone extending who use staying at your friends house. The TM30 needs to be done within 24 hours of arriving at the property I believe.
I have been asked for a flight booking confirmation in the past so I think it really comes down to the embassy your application goes through. If you have no reason to suspect you'd be rejected, I'd book the flights first.
You should be fine. My work rotation has me away from Thailand for a month and then in Thailand for a month. I've been asked questions a few times but I've always been able to provide the correct answers. I think they are more interested in the people that spend most of the year in Thailand using border bounces and extensions.