I have had over 5 years of experience helping clients in Africa to publish their content in various format and I have sound knowledge of e-commerce stores.
This is an interesting question because there are thousands of ways or methods to use to fulfil this singular project. In order to help you derive an answer to aid your decision making, I will ask you: 'What is your main goal or objective for an e-bookstore site?'. Are you looking at scope of distribution- reach? Are you looking at purchase fulfilment?
Your 'process' of achieving the desired objective should be your least concern. If ever you will be concerned about the platform to use then your concerns should border on cost, security, reliability, availability, etc.
If I was the one setting up an e-bookstore, my main concerns would be: 1. Distribution scope - in which case I will be looking for a platform that would afford my ebooks or content the widest reach possible. An in that case, I will be looking in the direction of Amazon platforms. Amazon has a wide reach and there is no need my reinventing another wheel in this regard.
In terms of relaibility, security, availability, etc the Amazon platforms have it.
Shopify is also a good platform and should get you up and running fast. If you would resort to WooCommerce , then your costs of development might shoot up since you might need a developer services to help you integrate the WooCommerce plugins(otherwise you might estimate the cost of time you employ going the DIY route). When you sum up the costs, then going the Shopify route is preferable seeing Shopify already has DIY tools that can easily get you started. Compared to Shopify, I personally think BigCommerce is more affordable(this might be arguable).
In summarizing, there is no need building from the scratch since that means 'reinventing the wheel' plus its attendant costs so going the Shopify/Amazon/BigCommerce route seems better.
Back to my Scope of Distribution factor which is key to the success of online e-book distribution, (after all, you aim for an e-bookstore is not charity but for making profit), you might as well explore the 'new marketplaces' such as hosting and distributing your ebook content via Googleplay, iTunes and Amazon stores since these are already have huge 'viewership'. That means you can distribute your ebooks in 'app' formats or pdfs.
Your end goal should be to make ROI of your investments.