While the set of discrete transistors may occupy a volume thousands of times that of the 555 or 741 die, the difference in size is largely one of packaging.
Here is an Xray through a TO-92 2N3904: https://www.flickr.com/photos/59935244@N03/5475873168
As you can see, the actual die is tiny– only about 0.5 mm (.020 inch) across, including the areas used for wire bonds. A modern 555 variant, the TLC555, lists its die size as 1.65 x 1.27 mm
(source: http://www.ti.com/lit/ds/symlink/tlc555-die.pdf ). So, a naive estimate would be that one transistor has about 1/8 the area of a whole 555.
Now, take a look at the die for that TLC555. There’s a photo here: http://www.bunniestudios.com/blog/?p=3542 . The big black circles are the wire bonds. And, there are several very large areas that look like intersecting combs. THOSE areas are the power transistors that handle the outputs. Yes, some of them are 1/8 the size of the die, or close to it. And, that’s on a modern chip — a “shrunk” die, based around super-efficient mosfets, not big and clunky bipolar transistors like the 2N3904.
So, a first inspection suggests that the actual area of the power transistors on the original chips is of the same order of magnitude as the area of our discrete transistors. It’s certainly not a difference measured in the hundreds or thousands of times. On the contrary: the sizes are quite comparable.
Getting back to your original question: Could you replace some of the transistors with more powerful types, and make a 555 or 741 with much higher current carrying capability? Absolutely! Just watch the rest of the properties of the transistors, to make sure that you’re keeping with the same kind of device.
It is certainly possible to make more efficient devices than the 2N3904/6, through modern fabrication techniques and using larger areas.
I don’t have any specific data about its die, but given that the ZTX968 is about 12 times the price of the 2N3906 (including packaging costs, which are fairly constant), it would make perfect sense economically if the die were 16X as large, 2 mm x 2mm, which would still fit nicely within the TO-92 package.
And yes, often smaller devices are preferred, because they have lower capacitance, and can be driven more quickly.
As to our particular choices: the 2N3904 and 2N3096 are simple, inexpensive, and common “general purpose” transistors that work well for these kits in most respects. There are a few places here or there that using a specific transistor with higher current or voltage characteristics would have been helpful, but we eventually decided (for both kits) that the simpler BOM was the better option.
