I ask it here because I think that emonSD have some configuration that block some apps to load on startup. Because I installed vncserver and I have to run it every time, and the samething with openhab2, by default when I reboot the pi is stopped, when I run it works fine, until next reboot.
What version emonSD are you running? Ir your running the latest emonSD30Oct18 built then install should be straightforward, although I have no experience of pixel desktop myself. emonSD-30Oct18 is based on Raspbien Stretch Lite.
Should not make any difference, Emoncms is lightweight and the RasPi3 is powerful.
There is nothing in emonSD to block apps at startup.
The only way an app night not run is if it requires a folder to be created in /var/log. Since /var/log is mounted as in memory tmpfs on emonSD, after a reboot all the contentents of /var/log/ is lost. We used rc.local to re-create the required folders on bootup Some services will make their own log files/folders if they don’t exist.