After you are done with georeferencing and one step before the rendering, it is possible to decide, whether you want to save your maps as Folder, as an MBTiles file or in a form of a GeoPackage. Each option has advantages and disadvantages regarding the speed of serving tiles, the simplicity of manipulation with output and viewing software support.
Folder contains a structure different tiles sorted into directories according to the zoom levels. To load folder on the hosting server takes longer, but the response on the website is then faster.
MBTiles is a single file, that can be easily loaded to any hosting and the upload time is shorter. However, the response for the users of your website is a bit slower than for the Folder structures. MBTiles are also suitable for imports of the maps into mobile devices.
GeoPackage is an exchange format standardized by Open Geospatial Consortium. It is also a single file, that can be easily loaded to any hosting and the upload time is short. Apart from Mercator projection, GeoPackage supports other coordinate systems, which are often country-specific. The generated GeoPackage file (.gpkg) is compliant to MBTiles format which makes it compatible with many viewers and software tools. Note that GeoPackage is limited to 8-bit color depth.
Direct upload to Amazon S3 or Google Cloud Storage from MapTiler Desktop supports GeoPackage.
If you render smaller maps or maps for your mobile device, use MBTiles or GeoPackage, depending on your preferences or software support. For larger maps and requirements for a fast access from end users, render into Folder and use a stable and fast hosting solution.
For output file format in command-line, see the MapTiler manual.