Does it make any sense to use both?
Depends on what “use” really means.
Usually, you shouldn’t need to use the avast! Virus Cleaner at all. Besides, if avast! resident protection detects a virus supported by the avast! Virus Cleaner, it offers you to start it.
What exactly do you want to do? 
well… I’ve had this trojano-247 (or still have…?)
I’ve run scans that found nothing with Home edition, but then found something when running a scan including the archives, plus some other files it said it could not scan…
I then found out about the Virus Cleaner, so I thought why not run a scan with that too…
But I got your point…
The stand-alone virusCleaner features a list with supported viruses/trojans/worms, and imho Trojan-247 is not on it…
→ http://www.avast.com/eng/avast_cleaner.html
In fact the stand-alone Cleaner only “CLEANS” worms and 1 “true” classic Virus
There’s a list of malware supported by avast! Virus Cleaner on the corresponding web page - there’s no use to try it on other viruses (such as Trojano-something), it won’t work.
:-[ah…uh…ok…
But can consider I’ve gotten rid of that trojan if several scans of Home edition don’t find it anymore?
Also, is it important to re-activate system restore, what if I leave it disabled?
I think you can say it’s gone. Of course, I suppose you have a fully updated operating system; if not and the virus explots some kind of OS vulnerability, it may come back later.
It’s up to you to re-activate the system restore… some people find this feature useful, the others useless. Decide
After I had a virus I left system restore disabled as for some reason it had 42000 files in it, used to take ages to do scan, I certainly would not use it again