That is my observation and it is an indication the problem is likely to be on the SailfishOS Android App support side. As part of this code is closed (and proprietary) as far as I know, we cannot track the mentioned calls in the source code to find more about them?
@anon48373651 @dschwert thanks for your contributions to the issue.
I do have a scanning device as backup, so I recommend that as well.
Scanning also works in the app, if the app is activated.
I was curious about this and thought a bit about how to trick the toolchain into taking inputs without invoking the keyboard layers. If you want, you could try this in the SFOS terminal while the PhotoTAN app is open and its input field has focus:
devel-su appsupport-attach /system/bin/input text "YOUR-PIN"
Android’s “input"-binary basically behaves like a USB keyboard, as far as I understand it. You can send it stuff and it then “types” it into whatever input field is active at the time. If that works, one could actually make a Patch in which you enter your PIN in a SFOS-UI and it then gets handed to the PhotoTAN app in AAS. Bit hacky and not exactly elegant or a secure architecture, though. 
(I’m not entirely sure if this works when your AAS window is in the background, so maybe best try it via a SSH from your computer while the PhotoTAN app is open on the phone).
Thanks, that’s working.
Afterwards, it might be a good idea to clear the shell history:
rm ~/.ash_history
Not a real fix, but a nice and much better workaround:
Use FUTO Keyboard. It comes with a “Show Keyboard” in the Top menu.
Tapping on the Keyboard in the Top menu shows up the keyboard, letting you to use it in apps that normally does not show the keyboard.
It’s available through OpenRepos.net (and via the Storeman app)
Thanks for adding this. I can confirm that it works.
One minor issue remains: with the standard keyboard layouts, the backspace <x| does not work. So if you mis-type, just go back and start again. If actually the FUTO layout is selected, it works.
Ask Jolla to fix that 
Had the same problem with newest Commerzbank Phototan app from Aurora Store while setting up my new Jolla Phone.
The app worked on my Xperia10II before, so I checked the version running there. After installing v10.0.0 on Jolla Phone, everything works fine. So I suspect they changed something in newer app version.