I would like to go to Thailand for 90 days. I plan to apply for a 60-day single-entry tourist e-visa and extend it once I get there. If I book outbound and return flights 90 days apart and upload the booking confirmation as document no. 4, can my application be rejected because my return flight is not within the initial 60-day period?

Some embassies and consulates want a ticket out of the country within 60 days to apply for a single entry tourist visa.

If needed you could use a one way ticket to anywhere to meet the requirement.