I understand that extension of stay on a multi entry non-immigrant 'O' visa is done by leaving and re-entering the country every 90 days. My question is, if I plan to apply for retirement extension of stay, (assuming I am over 50 and have required money in Thai bank etc), are there any advantages or disadvantages in using this option on the 1st 90day application or the last 90day application or any time in between.

The advantage is you no longer have to make any border runs - total cost 1,900 baht (unless you plan travel). The disadvantage is you paid for a multi entry visa that you do not need (but unless you plan frequest travel it is probably cost effective to go extension early rather than later).