In my recent experiences, it seems a site that uses anything but a stock install of WooCommerce should be afraid to upgrade. Custom templates are permitted but tend to break on upgrade, just had a payment gateway break this week because of a change Woo made (I've read support threads of several payment gateway plugins having issues). I love the software, but I think they could do a better job making sure templates and expensive payment extensions work with the latest version. People can't afford to have downtime. Writing to their support takes them a week to reply and even then, they rarely give answers.
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