See, if it is possible to drop Nautilus as a dependent from the ppa. Nautilus can be uninstalled after, but that would uninstall the meta package uubuntu-unity-desktop. The Unity install can live without the meta package, but autoremove would try to uninstall the following,
apturl apturl-common fprintd gir1.2-accountsservice-1.0 gir1.2-gck-1
gir1.2-gcr-3 gir1.2-gdesktopenums-3.0 gir1.2-gdm-1.0 gir1.2-geoclue-2.0
gir1.2-gnomebluetooth-1.0 gir1.2-gnomedesktop-3.0 gir1.2-gweather-3.0
gir1.2-json-1.0 gir1.2-nm-1.0 gir1.2-nma-1.0 gir1.2-rsvg-2.0
gir1.2-upowerglib-1.0 gjs libcue2 libfprint0 libgif7 libgjs0g
libgnome-autoar-0-0 libgsf-1-114 libgsf-1-common libmozjs-60-0
libpam-fprintd libtagc0 libtracker-control-2.0-0 libtracker-miner-2.0-0
libxcb-res0 mutter-common switcheroo-control tracker tracker-extract
Some of them are needed, so can be manually installed. Maybe those that are needed, should be put in as dependencies in the ppa.
The other matter, can the newer Nemo 4.06 put in the ppa? Maybe David, @fossfreedom can help in that? Maybe, even better, if you can get Nemo 4.2.3.