Not exposing things in the UI is not necessarily a problem (it depends on the program and on other stuff), although it can be (especially if it is not documented). I had not used the program you mention, although it does seem a problem in the way you mention, although someone who wants to add it into the UI could hopefully do so if it is FOSS. However, one potential problem is sometimes if it is a text-based format, writing such a format (in a way which still remains readable rather than messy) can sometimes be more complicated than reading it.

(The TEMPLATE.DER lump (which is a binary file format and not plain text) in Super ZZ Zero is not exposed anywhere in the UI; you must use an external program to create this lump if you want it. Fortunately that lump is not actually mandatory, and only affects the automatic initial modifications of a new world file based on an existing template.)

However, I think that human readable file formats are harmful for other reasons.