The reason is a little deeper.
There are many things one wants a spreadsheet to do involving the copying or transferring of information in, into, and out of, it. Sometimes "just because" and in any spreadsheet, sometimes in a particular spreadsheet due to its program's features, or even choices one has himself made. And Excel supports some/many of these things.
However, the information it needs to carry with the data, as part of the data/formatting/etc., or to enable the full range of uses, INSIDE Excel that you may wish to put it to, is very often far more than the Windows Clipboard can have and still be "true" to its own conception.
The Clipboard does not really distinguish between one bit of textual information representing data Excel might place in it and textual information representing, perhaps, formatting, that Excel might place in it. Formatting, in particular, would be partially supported, partially not. The Clipboard will pass font information for example, and likely has a way to know a bit of text is that kind of thing. Excel can pass its own Copy-ing to it in the required form. But maybe the Clipboard does not have a way to mark "Center Across Selection" or "Merge Cells" information in a standard way that other programs can recognize and use properly or discard.
Excel must keep that information in its Copy-ing, so as to be able to use it in its own operations. But it cannot at the same time be passed to the Clipboard without it becoming weird and stray text added to the actual desired text. (The converse/corollary/whatever of that is seen in copying a cell to Paste its contents into, say, a website's login entry boxes and Excel having added something to cause a carriage return/line feed to be added that may or may not be ignored.)
So Excel uses its own internal Clipboard. It takes whatever "true" Copy Excel considers having been made, with any information it feels it might need, and holds it until one Pastes. If pasting inside Excel, and often in other Office programs, though often not, the information can be used fully. In Excel, one might see the program extract the two cells' data and formatting that you selected using Ctrl-Click and decide how it should place it where you are pasting it. So you get the two cells and their formatting with the simple paste, and while it COULD have been written to keep their relative locations, say rows 2 and 6, they decided such a thing should be pasted as if originally contiguous. Well... choices. (Useful to me as often as aggravating. I imagine that varies for others.)
At the SAME time, Excel writes to the Windows Clipboard (distinguished from its own internal "clipboard") what the programmers figured should (and can) be written to it. They did not necessarily think of every variation on every theme. In your example, they clearly figured uses outside Excel would be better served with all the contiguous data marked by the start and stop cells. Or that is, and/or was, the standard thought at the time. Or it was never thought of at all. So many possibilities.
(This internal/intermediary "clipboard" is, by the way, the source of difficulty that leads to the weird error message about how there is an error with the clipboard but you can still paste into other programs.)
So it's likely in no way a "bug" but rather a chosen feature, an incidental feature, or a thing that was never thought of so can't be right ("feature) OR wrong ("bug).
Clearly though, Excel is aware that if a row, say, is hidden/filtered out/set to 0 height is undesired in a Paste, even one pasted outside Excel itself. Maybe the thinking was that a "positive step" to indicate those things were undesired was good enough to send a data package to the Clipboard that does not include such. All those situations might actually be achieved by each of them setting the row height to 0, and so maybe Excel looks for that characteristic. The use of Ctrl-Click to mark particular cells for copying, coming years and years later, might simply not activate that removal before writing to the Clipboard. Might be as simple as that.
In any case, you might make an entry on the current UserVoice web tool. For a veyr long time it looked like Excel people just made nice noises, then completely ignored any entry. But recent changes suggest that they did pay attention, just that it takes 10-20 years for them to act upon them. (Sigh...) But one never knows. That place IS the official place for such suggestions though, unless your employer (or you) pay tons of money to be on a support plan.
