Yep, this is how I use it. I have another ebike for everyday use.
Not sure about the two-bikes concept though, because long-term bike parking is still a huge problem, security-wise, esp. for ebikes.
The NS (Dutch National Railway) sells a secured bike storage subscription starting from 75 euros a year. And you can do it cheaper if you use your bike frequently because at some stations the first 24 hours are free.
And if you have a cheap bike that you use just for your commute you can also just put it in the free bike storage and only move it secured if you know you will be gone for >2 weeks or whatever the limit for free storage is.
Paris is also not flat, so unless you're super in shape it's difficult to use a non-electric bikes (depending on the journey, of course), and ebikes tend to be stolen much more than regular ones.
In other French cities, I don't know enough to have an opinion; I think Strasbourg is a little bit better.
That being said, I know people who have done the two bikes thing, or at least one bike that "lives" at a railway station, for a long time and not aware of them having any problems.
I guess the appeal of the folding bike is more for irregular or infrequent trips.
Totally agree on the freedom aspect. Bicycles are ideal for inner city travel. Cars should be banned. I often use public bicycle shares when I travel now which is great because you don't even have to fold/carry or lock the bike up anywhere.