What customization can't be possible with SuiteCommerce? I have Very complex customization on PDP(Lot Number Items need to fetch) should I go with SCS or SCA?

Your question is too vague to answer, it really depends on what you want to do. Generally speaking, we do not recommend/allow customisations to a SuiteCommerce site that involves modifying the core code, that is, the code that we provide to you into the bundle. We expect any SC customisation to sit on top of the existing code, and to plug into it using the extensibility methods we provide.