How robust Shopify theme customizable is? [on hold]

I've been asked to design an e-commerce website for a retail business dealing with beauty products which is going to use a Shopify theme. Since I have no experience in setting up a website using Shopify, I'm in a bit confused state to start the design work. I wonder there must be some limitations and some important factors that should be kept in mind while designing the webpage which is going to use a Shopify theme. I googled for the same, but could not find solid resources.

Lets say I would design the website that my client is completely satisfied with. But would I be able to customize the Shopify theme into the exact design and layout that I came up with? I do have knowledge the HTML / HTML 5, CSS / SCSS, jQuery, Frontend framework [Bootstrap / Foundation]. Will I be able to customize the theme into my own design and layout using those knowledge?

All in all, what I want is to let my client purchase a Shopify theme and I would customize that theme into my own version of design and layout. The main purpose of using Shopify theme is to use the backend part [CMS, Cart features, Payment processing etc]. Will that be possible on designer's end?

I look forward to having ideas from the experienced fellows. Resource links are also welcome.

Thanks in advance.

--Ishwor