I will answer with a simple question: When's the last time you had to press a function key and a number key at the same time?
When it comes to split keyboards and other kinds of shaped keyboards, smaller is usually better to a point. Standard keyboards are usually more fixed in place and as such, the size doesn't matter as much as long as you can still reasonably use it.
Well yeah that argument is flawed if you don't account for the position and common use of keys. I know it's a bit of a arbitrary rule. You wouldn't want to press a number or enter on the same key, nor are they even close to each other. However, two keys that occupy common outcome with a different "function" that are also close to one another have the opportunity to be combined either contextually or with modifiers. I will also add that these keys being on the edge of keyboards also gives an advantage for combination to reduce size. You could also bridge the number pad keys with the function and number row keys. However, the purpose of the number-pad is more than just numbers and some symbols, the primary purpose is the for the layout (at least in my eyes) to improve usability and speed.
It's not a definitive answer that has only a single logical path, merely an answer/explanation that codifies the why based on common use and anecdote.
However, you do bring up a good point in your original post. Most of the time, it's programmers or "power users" that makes sense to have this contextual combination layout. For normal people, you assume every key does one thing and look for it on the keyboard when you need it.
The real answer is a combination of above and cost saving. If developers of keyboards can not include ~13 keys (to include tilde/grave), this saves on many aspects of design, hardware, and software. It's kind of why some keyboards also don't perfectly mirror all of the modifier buttons across the keyboard. Most people probably don't even know/use the right alt key. Shit, my right alt key isn't even a proper alt key; it's my symbol input key!
I didn't intend on typing so much, but I hope this clarifies the "argument" in my first post.