do you prefer native POS ecom integrations or custom API webhooks for retail sync?

Im debating now what is the general agreement (and usually the better choice) regarding omnichannel data flows for small to mid sized specialty retail. when you are building out a web presence for an existing physical store do you find it better to use the point of sale companys native web integration or write custom webhooks to handle the stock adjustments. long story short, im looking over a project for a boutique beverage client and their current register setup uses a WinePOS backend which has a built in FTP and API pipeline for pushing live inventory counts to digital channels. it seems clean enough on paper since it handles the tax rates and regional compliance stuff out of the box.

but a part of me always worries about being locked into a proprietary ecosystem if the client wants to scale up to a completely custom headless commerce build later on. do you guys usually just run with the native platform tools to save deployment time or is it always worth building out a custom middleware database from day one? would appreciate some insights, thanks