Maybe. 
The long answer is: right now, reform-tools only ships one thing in /etc: a symlink from /etc/kernel/postinst.d/zz-reform-tools to /usr/share/kernel/postinst.d/zz-reform-tools to make the kernel postinst hook compatible with kernel releases before they switch to supporting hooks in /usr/share/kernel. In earlier days, all of this used to be shipped by the reform-tools package in /etc:
/etc/reform-desktop-help
/etc/reform-help
/etc/reform-root-help
/etc/X11/xorg.conf
/etc/skel/.local/share/rofi/themes/mnt-reform.rasi
/etc/skel/.local/bin/reform-windowmaker
/etc/skel/.local/bin/kde
/etc/skel/.local/bin/gnome
/etc/skel/.ircrc
/etc/skel/.config/xfce4/terminal/terminalrc
/etc/skel/.config/wofi.css
/etc/skel/.config/wayfire.ini
/etc/skel/.config/waybar/style.css
/etc/skel/.config/waybar/config
/etc/skel/.config/systemd/user/waybar.service
/etc/skel/.config/sway/config.d/input
/etc/skel/.config/sway/config
/etc/skel/.config/qt5ct/qt5ct.conf
/etc/skel/.config/mpv/mpv.conf
/etc/skel/.config/gtk-3.0/settings.ini
/etc/skel/.config/foot/foot.ini
/etc/skel/.config/dunst/dunstrc
/etc/skel/.config/autostart/pasystray.desktop
/etc/skel/.config/autostart/lxpolkit.desktop
/etc/skel/.config/autostart/blueman.desktop
/etc/profile.d/reform.sh
/etc/motd-rescue
/etc/motd-full
/etc/firefox/syspref.js
How do users get these files these days? They are part of the system image and no longer get shipped by any package. This has advantages and disadvantages. The problem with packages shipping files in /etc is, that those files are config files for dpkg. This means that the user is allowed to modify them and they do not get removed even after the user uninstalls the package (they have to “purge” the package if they want config files to be removed). The disadvantage of not shipping these files in reform-tools is that it is now impossible for reform-tools to ship updates to these files. But then, updating these files is exactly the problem that we would have if reform-tools would ship them. Because if the user modified them and then reform-tools modifies them as well, the user would be presented with a conflict and would have to resolve that manually somehow, which is annoying.
Luckily, a lot of stuff that was in /etc can be moved to /usr. For example, the kernel hooks in /etc/kernel/postinst.d can soon live in /usr/share/kernel/postinst.d and there they are not config files any longer and not supposed to be updated anymore. For the files in /etc/skel, the issue is, that packages in Debian (with the exception of bash) are not allowed to ship files in it: Lintian Tag: package-contains-file-in-etc-skel So to upload reform-tools to Debian proper, those needed to go.
Back to your original question: can they be deleted? It depends… if you do not plan to add a second user to your machine (like a friend or family member) then the files in /etc/skel are quite pointless because their only use is to populate the $HOME of a new user. Furthermore, if you want to create a new user, you might want to consider using the updated files of /etc/skel from the reform-system-image repository. On the other hand, having the files in /etc/skel also does not hurt. They are very small.
If you delete them now, dpkg will complain that suddenly config files are gone. In case of your example, the dpkg --verify output will look like this:
missing c /etc/skel/.config/sway/config.d/input
missing c /etc/skel/.config/wayfire.ini
If all you want to do is to get rid of the two lines in your “the following files differ” output of reform-check then you would have to restore them into a state that matches the md5sum stored in /var/lib/dpkg/info/reform-tools.md5sums. If you tell me which md5sums you have for /etc/skel/.config/sway/config.d/input and /etc/skel/.config/wayfire.ini then I can give you links to the correct content.