BaseElements is available as FileMaker files for use in a copy of FileMaker Pro or Pro Advanced, or as a standalone runtime application. Both have their advantages and disadvantages.
The FileMaker files are .fp7 files in BaseElements 3 or .fmp12 files in BaseElements 4 or later. These require a copy of FileMaker Pro / Advanced to run.
But also the fact that you're running FileMaker means you can modify the BaseElements files. You have complete access to alter the layouts in BE, or to add your own scripting logic to any of the files. As well as that you can create your own external files that reference the Data file and build your own UI or re-use the BE data in any way you see fit.
The runtime version of BaseElements has the advantages of allowing you to have a separate application for BaseElements and switch between it and your solution running in FileMaker Pro at will. The plugin is already in the correct location, so there is nothing extra to install. Also because BaseElements requires a fairly new version of FileMaker Pro to run, if you don't have this version of FMP, you can use the runtime to import a DDR from any version of FMPA.
However, the runtime doesn't allow you to use Layout mode or edit Scripts. You could though build an extra file with your own UI or other details which links to the data in the BE runtime. The runtime BindKey is just "BaseElements", so by building a runtime of your own with the same key you can add extra files into the BaseElements runtime solution.