This is how manufacturers decide what options and vehicles are offered in which markets.
Long before the vehicle starts production some generic spec levels are defined. These are created from a combination of historical knowledge and predicted demand. These vehicle configurations are important as they form the basis for the profitability of the model over its lifetime - every manufacturer has a target ROI (Return On Investment) for the models it makes. There are ROI targets for options too. Then the engineering and design departments create designs and configurations which fulfill the ROI targets. We end up with a set of "base" vehicles and a pile of configurable options, some are market specific, some are legal requirements etc. and not visible to the customer, some are options that can be chosen by the customer.
From all these options we tailor the offer for the markets and their local requirements. Some markets have customers who want to configure everything and are prepared to wait (e.g. Germany where the configuration can be fiendishly complex.) and some markets have customers who want to drive a ready built car off the forecourt (e.g. USA where the majority of vehicles are ordered by dealers for stock and loaded with options). There are also markets where the customers don't want to be overwhelmed with choice or where the manufacturer wants to limit the available option combinations (RHD markets like the UK for example). In these markets options are often bundled into packets or reduced as the market is small and a built vehicle can not be readily sold into another market. RHD markets are usually constrained or bundled for this reason.
After all this is done and the predictions of take rates for options and models is completed the component suppliers are contracted to provide an agreed number of components over the lifetime of the vehicle, plus a percentage of spare parts. There are also options into the contract for additional supply or a reduction of components which are used once the real-world data starts coming in when the vehicles go on sale.
When the vehicle is nearing end-of life, the offers in markets can be cut/changed to ensure all the contracted parts from suppliers are bought in the volumes agreed - which is why special editions appear, or options end up bundled together - or even withdrawn. It is to do with balancing the contracts with parts suppliers. Sometimes models are even chopped from the line-up or removed from specific markets - but it is all to do with balancing the books and the supplier contracts to phase the vehicle out as cost-effectively as possible.
It could be for example that VW have bought all the manual roofs they contracted, but still have an outstanding quota of electric roofs to get rid of - hence models with manual roof might get dropped entirely. The only people who know really know why are the VW product planners.