Oleks, 

apologies, but I can only add a comment on your second point, as I don’t quite get the first. 

I think ‘ the administration can so decide ….’ or ‘ the administration can decide so …. ‘ is an excellent way to reformulate in English the purpose/use of  ‘ le ‘ in French in this example. I probably would have gone with ‘ that ’ but I actually think ‘ so ‘ is more expressive here, and can be stated in the same word order as in French. Without the prior context, ‘ so ‘ does fit the bill !

The difference between the two sentences, in a nutshell, is that the first one requires the pronoun of the direct object (le), whereas the second one needs the pronoun replacing an indirect object introduced by de (en). The root goes back to the respective verbs:

dédider qqc. --> le décider

il feut respecter les limites de qqc. --> il faut en décider les limites

Oleks,

the neuter object pronoun ‘ le ‘ can be used to replace a previously expressed ‘ idea ‘, as noted in the lesson you linked. (See additional information in Laura Lawless link)

That is, ‘ le ‘ is replacing something said/written prior to this sentence. It would be helpful to have the full context, but the fact that the sentence in which ‘ le ‘ is used as a neuter pronoun contains a prepositional de in ‘ faire partie de qqc ‘ ( or a partitive in de la ), does not preclude the use of ‘ le ‘ to replace the previously expressed idea, and does not allow/require the use of ‘ en ‘ in its place.

‘ En ‘ can replace a phrase introduced by the preposition ‘ de ‘ - in the second example the prepositional phrase arises because it is  ‘ les limites de qqc ‘. This is the construct that gives rise to the use of ‘ en ‘ replacing the ‘ de qqc ‘.  

In the context of this sentence, it would otherwise end with ‘ les limites de la liberté d’expression ‘ but instead of being written in full, ‘ (de) la liberté d’expression ‘ is replaced by the adverbial pronoun ‘en ‘.  

https://www.lawlessfrench.com/grammar/neuter-object-pronoun/

 https://www.wordreference.com/fren/limite

 En can replace de + [phrase] (French Adverbial Pronouns)

Thank you for your answers. I appreciate it

Could it be so that first sentence is a compound and not complex one, which means that we do not replace anything from subordinate with pronoun "en" since we do not have this subordinate clause at all? 

After more focused look I realized that "le" of the first example does not have any semantic connection with second part. It's just "Yes, administration can deside so..." And the sense behind "so" is hidden in the context which is not given to us