I implemented the "fix" that caused this secondary issue. In some ways this goes to show the problems that too much nannying and hand-holding of the player can cause
(For instance I'm of the opinion that autotargetting does not need to get any more sophisticated than it currently is, whereas others would like to see, for instance, area spells selecting a target that takes in the maximum number of enemies in the blast radius, or figuring out what coordinate is likely to cause the highest amount of damage, or knowing which monsters are highest-priority targets, etc. Do we really want the player to never have to make a targetting decision? I could ask: for folks that play FPS games, do aimbots improve your enjoyment of the game?)
Sorry, that was getting slight off-topic. The two relevant things that changed were:
1. When reading an unidentified scroll, if it brings up the inventory menu, that list is now filtered to only things that are possibly valid scroll targets: armour, wands/rods, and any unidentified items. There is an additional clause that the scroll you are reading gets filtered out. Previously everything in your inventory was listed even though a lot of items would never have a reason to use any scroll on them.
2. Previously you could press the letter of something that wasn't in the list, and the scroll would get burned up anyway (but not identify). Now you are completely restricted from selecting non-list items. This change applies to all inventory selection menus, not just scrolls - so it fixes a few slightly strange messages and cases that could result from mis-hitting a key etc.
Some other consequences (like the melded equipment thing) were just additional issues that I fixed while I was working on this.
The contentious part of this then is whether a scroll can be used on itself. I can see the argument that if it's a stack you should be able to use the scroll on the other copy that you have. On the other hand this is actually wasting a scroll anyway. This early in the game you are sure to a fairly high probability now that this is an identify scroll, so allowing you to use it on its own type doesn't really add up to much difference. I generally don't read-id scrolls until I have some other items I could use them on anyway (surely you had armour you could use it on ... or did you already identify enchant armour? ... in which case you're now even more certain that this was an id scroll...)
Looking again at BlackSheep's report (
https://crawl.develz.org/mantis/view.php?id=5868) I realise that it did specify "Singleton un-ID'd scrolls". The thing here is that this doesn't fully fix the issue described in the report because it means if you have a stack you can easily waste the scroll by accidentally double-pressing the letter as BlackSheep did.
If we go with ">1 scroll and it can target itself" then probably the solution is a "Really use [scroll] on itself?" prompt.