Usually there are 2, perhaps 3 situations to be distinguished:
(1) "Raw assets" as are loaded by an editor for the purposes of being viewed and perhaps integrated into the project,
(2) "runtime assets" that are loaded by the game engine,
(3) and perhaps "runtime assets" that are loaded by the game engine, either provided for hot-swapping, software updates, or modding.
Raw assets can be stored in the native file format of the DCC or in a common interchange file format (e.g. Collada for meshes), obviously to have a chance to re-load it into the DCC and make changes. These assets are further given by individual files, although a single file may provide more than one asset.
Runtime assets are usually provided in a game engine specific file format. The purpose is to yield in fast loading, which means a binary format because it is more compact but also requires less pre-processing in the game engine. The tool-chain is responsible to convert from raw assets to runtime assets.
With respect to the normal game play runtime, one don't want to have to open one file per asset. This is because file opening costs time, and having many more or less small files consumes more storage footprint. The solution is to use some kind of package file format. It further allows assets to be sequenced which in turn allows for shorter load times.
Now, with respect to hot-swapping, updates, and/or modding, storing assets in a single big package is bad, because replacing an asset in a package is often painful. A solution is to use the same file format but allowing for single, additional files so that the content of these files override the corresponding content of the regular packages. The runtime asset loader can handle this for example if the overriding asset files are stored in a dedicated file directory apart from the main asset files.
With packages the question of different file suffixes for runtime assets vanishes obviously. Further, it it easier for the runtime asset loader to handle a single file suffix. It has to investigate the file content anyway. So for me using a single suffix for runtime assets is a good way.
Just my 2 Cents.