Are "violation points" applied to EU licences outside of their home country?

There is no EU-wide system to handle penalty points and driving bans. In fact, those systems are probably more diverse than you realize, in some countries you 'lose' points until you have none and must surrender your license, in others you 'gain' points and exceeding a threshold has consequences. The number of points and thresholds for various offenses vary too and some countries do not even have a penalty point system.

What does happen is the following:

• Fines are increasingly enforced across borders. Your home country might reveal your address based on your license plate number or even go further than that and collect on behalf of the other country. There is a framework to encourage this at the EU level.
• If you reside in another EU country and drive there with your original license (which is perfectly legal in many cases) and commit an offense that results in a suspension or penalty points, you can be forced to exchange your license for a local one.
• Even if you don't reside there, you can of course receive a ban in the country you are visiting. This ban won't automatically apply to your country of residence.
• If you commit an offense abroad, you can get some penalty where you live, in some cases even if there is no penalty point system where you committed the offense, but that's entirely up to each country. Conceptually, it's not a foreign punishment being applied by the local authorities, it's the local authorities applying their own punishment based on information they got from another country. There is no exchange of "data on traffic points" or any EU rules on each country is free to do what they want with any information they get about what you did elsewhere. Anecdotally, I think that Switzerland is for example very aggressive with this. Other countries don't do it at all.

Point systems and driving bans are, unless national law says otherwise, country specific. There are no EU/EEA wide regulations for this subject.

What will happen, if you as a Czech resident with a Czech driver's license manage to get so many violation points in Germany that they qualify for a driving ban, the German authorities will issue a driving ban for Germany.

The Germans may also inform Czech authorities about fines, points and driving bans, but it is as I said, up to Czech law and Czech authorities if that will have any consequences for you and if applicable what they do.

Even if it may sound illogical, the same principle (national jurisdiction) also apply the other way around. If you are a German resident with a German driver's license and the German authorities issue you a driving ban, this driving ban is per default also only valid for Germany. Unless restricted by national law, you may still be allowed to drive in other countries.