Yes, RPGT is basically a type of witholding tax. Refer to the following from iProperty:

"When to pay RPGT in Malaysia?
For locals and permanent residents who sell off property, their lawyers will retain 3% of the property’s selling price/disposal price when the purchaser pays the first deposit to buy the property for the purpose of RPGT payment. For non-citizens & foreigners, this retention rate is 7%.
Your solicitor will make the payment with necessary forms to Inland Revenue Board within sixty (60) days from the date of the sale and purchase agreement to meet the RPGT payable."

Therefore, RPGT is withold by the lawyer for LHDN. Based on my understanding, you (or your lawyer) just need to file addtional documents with LHDN basically showing proof you hold your property for more than 5 years and you can claim back the money or top up if the witholding RPGT is insuffcient to cover.

For us yes. For gov no, you collect first and place the burden to proof on the seller itself. Sometimes people even forget to claim back this money. Very unlikely but it happens. Just the same with your salary PCB. Company withold it and submit to LHDN, and if you got sufficient tax relief you can claim back from LHDN. Same mechanism.