How to white labeling a wordpress commercial theme

Pricing for different tasks that require the same amount of time from you tells the Customer (and your subconscious) that you're working at a 5 on task x, but working at a 9 on task y simply because it costs/earns more. That seems to be a disconnect. Your time is your most precious asset, and I would charge for it whatever you're doing. If you build a site, and they are happy with your dev fee, but feel like you should charge less for SEO, simply let them find another SEO guy. That's their choice, but YOU are worth $xx.xx, no matter what you're doing. Also, in general, take whatever you're charging and add 10% to it. If you're still busy, add another 10%. Let the demand level determine how much work you do, and at what cost.

Checkout is a high-quality WordPress theme by Array built for marketplaces of any kind. https://arraythemes.com/themes/checkout-wordpress-theme/ Let me know if you have any questions about implementation, and I'd be happy to setup a call.

There is a lot of points in your question which unless someone has the exact same setup as you - I don't think you will get the answers you are looking for. I believe you should limit it by asking yourself: What is the ONE thing the MLM plugin I am looking for can do so that it achieves the maximum amount of result to my business by using it? IMHO - it would be the ability to set commissions for the products you sell and award commissions to those affiliates that actually earn you sales. All other features, while nice, are ancillary features that from the perspective of the affiliate - don't really need in order to be successful. In that regard - I would suggest https://affiliatewp.com/. When it comes to running affiliate programs on WP sites, it wins out as the best in my experience. Hope this helps! Glad to assist any further if you need help.

Yes. https://docs.woothemes.com/document/configuring-woocommerce-settings/

Be careful when simply wrapping things into a mobile app. This can backfire on you and you could be presented with some very harsh edge cases. PHP isn't going to be encapsulated so much as the HTML/CSS/JavaScript. So keep in mind your mobile application could likely be in a position of requiring an online connection to work (because it must interface with your existing hosted WordPress site). This could also mean your hosting solution needs to be evaluated to ensure you can handle any increased traffic (and those traffic patterns could be different when coming from a mobile app that perhaps loads things the user doesn't see right away, accesses content that may not be cached, etc.). You want to ensure your server doesn't go down because then your mobile app would be "down" as well. That said... Things like Phonegap (web views) are a wonderful idea for utility apps because the performance is good enough for those (and hey even some games) and they end up being easily ported across many mobile operating systems. I would look into Phonegap, Appgyver (a new and totally awesome one because parts of it will utilize the native OS and your app will feel more responsive), Appcelerator Titanium, and perhaps even the new Famo.us one. Also take a look at the Ionic Framework for some further ideas about mobile UI and what you can do with these web view style apps.