The glyph names and how they behave (their glyph properties) are defined a big file called GlyphData.xml. Here is what the line for bismillah-ar looks like:
Here, you can see the name of the glyph and its properties such as the Unicode code point, the category, script, and writing direction.
And here are allahlong-ar and jallajalalouhou-ar.
For these, the Unicode code point is marked as legacy and the category is Letter, not Symbol. I am not sure if these differences are intensional or historic artifacts.
As you noticed, the current GlyphData does not contain all of the symbols you want. U+FDFF ARABIC LIGATURE AZZA WA JALL, for example, is not part of GlyphData yet. You can create your own GlyphData file containing only the new glyph definitions. For example:
<glyph unicode="FDFF" name="azzawajal-ar" category="Symbol" subCategory="Ligature" script="arabic" production="uniFDFF" direction="RTL" description="ARABIC LIGATURE AZZA WA JALL" />
or similar. Learn more about GlyphData.xml and how to edit it using the EditGlyphData app in the tutorial here:
We are happy to integrate these additions into the GlyphData included with Glyphs. You can either send us your proposed definitions here on the forum or contribute to the GlyphData file on GitHub.
If the GlyphData approach is too much work and all you want to do is define a handful of glyphs, you can also add a new glyph with a name of your choosing and define the properties with Edit → Info for Selection…:
The GlyphData approach is preferable when you want to reuse the glyph definitions across multiple Glyphs files and sharer them with others.