What due diligence should actually cover before you pay a deposit
Due diligence is not a formality you do after agreeing a price. It is how you find out whether the price was ever right.
The certificate
Get a certified copy and check it at the local land office (BPN). You are confirming three things: that the certificate is genuine, that the person selling is the registered holder, and that there is no mortgage, caveat or dispute recorded against it.
Zoning
Zoning determines what you may legally build and operate. A plot zoned residential cannot run a villa rental business, however many neighbours are doing exactly that. Enforcement is uneven — until it isn't, and it tends to arrive right when you have finished construction.
Building permit
PBG (formerly IMB) should match what is physically standing. Extensions built without permits are extremely common and become your problem the moment you take title. Compare the permit drawings against the actual footprint.
Tax
Ask for PBB receipts for the last five years. Arrears follow the land, not the seller. Also budget for BPHTB — 5% of the transaction value above the non-taxable threshold — which the buyer pays.
The boundary check
This is the one most buyers skip, and the one that causes the most litigation. Land area on a certificate is what was measured, sometimes decades ago, sometimes generously. Commission a licensed surveyor to peg the corners against the certificate drawing. It costs very little relative to the purchase and it is the only way to know what you are actually buying.
If a seller resists any of the above, that resistance is itself information.