To understand the differences, we have to look at the different goals of the two.
Or in other words: What do they want to do? What do they do? And how does it affect you as an end user?
In this answer I will speak of Firefox's Multi Account Containers and Firefox's Facebook Container as pretty much the same thing, because - as far as I understand it - technologically they are.
What do they want to do?
The creators of uBlock tell us here:
uBlock Origin (or uBlock₀) is not an ad blocker; it's a general-purpose blocker. [...] Ads, "unintrusive" or not, are just the visible portions of privacy-invading apparatus entering your browser when you visit most sites nowadays. uBlock₀'s main goal is to help users neutralize such privacy-invading apparatus — in a way that welcomes those users who don't wish to use more technical, involved means [...].
Firefox says this about their addons:
Firefox Multi-Account Containers lets you keep parts of your online life separated into color-coded tabs that preserve your privacy.
Rather than stop using a service you find valuable, we think you should have tools to limit what data others can obtain.
This sounds very similar, but the differences are in the details.
uBlock is focused on privacy on a broad scale and users sometimes have to hazard the consequences -> buttons can stop functioning, sites can break etc.
The Firefox extensions are the parent-version of a neat tool to ensure some privacy. You can still use all services. There can be some collateral damage, but rarely for the typical user. And it's all color-coded, weeeee!
What do they do?
uBlock Origin blocks these three types of annoyances: ads, trackers and sometimes malware sites, but can do a lot more. It has a pretty wide range for such a lean tool, but you have to be somewhat experienced to make use of the more interesting options like medium and hard mode. And if you do, sites will regularly start to break if you browse like most of the regular internet users.
If you take a look at the documentation I linked to, you will see what uBlock can do "under the hood".
Note: a lot of blocking by uBlock requires filter lists. The maintenance of theses lists is very difficult and tiresome and is done by a lot of nice people on the interwebz. Because they do it for free, sometimes trackers will not get blocked, because they are not on the list you are using. IMO that is not all too problematic, because the problem you as a user have stems from forming profiles, not from creating single points of information. If the contributors update the lists properly and you regularly update your filter list it is likely that the next time you visit a site with that tracker, it will not track you.
In the description of Firefox Multi-Account Containers, we find the following:
Each Container stores cookies separately, so you can log into the same site with different accounts and online trackers can’t easily connect the browsing.
and under the description for Facebook Container
What does Facebook Container NOT protect against?
This extension focuses on limiting Facebook tracking, but other ad networks may try to correlate your Facebook activities with your regular browsing. [...]
The big thing we can note: Firefox Multi-Account Containers neither block ads nor trackers. But this isn't what they were built for. They were built for separation or containerization. A lot of data is accesible for sites you visit across tabs - for instance: cookies.
Containered tabs - this is what we are looking at here - prevent this.
How does it affect you as an end user?
You can easily use both addons. I would definitely recommend uBlock (go for the hard mode). There are some restrictions that containerization brings to the table that can be helpful. I am not too knowledgeable about the inner workings of it though.
Conclusion: The two addons are very different, but that is very much okay, because they have different goals and I would say different audiences with different privacy needs.