It rather depends on any past history of repeated Visa-free entries. If you've been in and out several times a year, then you may have issues. If you're just coming once a year, no problem. Don't forget that 20,000 baht (or equivalent) in your pocket just in case asked.
Land borders are indeed limited to 2 annual crossings.
if you're on 2 separate bookings you WILL be entering the country. Not many airlines will through-check (interline) your bags to the final destination if they're separate bookings on different PNRs.