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"Is there a way though to eliminate Filemaker branding from webdirect so it appears like most high end web-sites."
Sort of, but you'll never have complete control over it, nor will you ever be able to completely remove all traces of filemaker (EG from the rendered source code).
Since each "page" in WebDirect is generated on the fly by filemaker, there is going to be no way you can modify the code that WebDirect spits out since it takes place at runtime. There are styling changes, and things like hiding menus and such that you can do to mimic a branded web app experience. There is also some options for "hacking" webdirect to customize title strings and CSS base classes.
If you want complete control of the UI though, you need to look at using CWP or the new REST API in order to have command over your front-end. In doing so, you face a daunting path of having to do a lot of heavy lifting to mimic the filemaker experience. So the decision rests on what is more important for your need: 1) The filemaker experience, or 2) the user interface. This is the usual conundrum of using WebDirect. Don't forget that licensing is also a consideration for WebDirect.
"Can search engines index data or URLs?"
No, because every view WebDirect draws is rendered dynamically. A search engine may be able to index your landing page URL, but it will not be able to garner any real information from that. You can also make a custom landing page with a robots.txt file that will ask crawlers to ignore your page.
"so it appears like most high end web-sites."
This is what makes WebDirect so great, but also so tough. Most "high-end" websites have teams of developers that are writing code to the tune of hundreds of hours per week. Giant trees of git repositories, testing suites, deployment plans and the like. Then you walk in as a single developer and create something incredibly dynamic and interactive in 1/10000th of the time and deploy in just a few weeks. So while webdirect is GREAT, and can take you very far in the "web app" space; you will inevitably hit a wall trying to stack up against a behemoth development team that has more resources available than you. I would definitely consider submitting a few ideas to the Product Ideas subspace here on the community with your ideas for taking WebDirect further.