Whenever you an ecounter the sequence el [verbo], it can be helpful to swap it out with the sequence el acto/la acción de [verbo] (the el generally isn't even necessary):
El estudiar por la mañana es mejor porque estás más despierto.
is equivalent to
El acto de estudiar por la mañana …
Verbs can take various complements without any problem:
¿Esta cosa? Comprarla me saldrá muy caro ahora.
Verbs are technically neuter, and agree in the neuter (which just happens to share its endings with the masculine singular). That's why we say "caro".
Where your example gets even more complicated is that instead of being just a verb perhaps with some complements, it also has an explicit subject. Most students of Spanish are told that to have a subject (certainly a change of subject) one must use a conjugated verb form, although that's not strictly true.
In your example, we have
… cuando el ser conocida una esencia por otra coincide con …
So here we can break this down as
cuando el ser conocida una esencia por otra coincide con
^---------------sujeto-------------^ ^-verbo-^
The subject is
el ser conocida una esencia por otra
| | | | |
| | | | +-> agente (sujeto si fuese activa)
| | | +-> sujeto del verbo nominalizado
| | +-> participio pasado (concuerda con el sujeto, esencia)
| +-> «sustantivo» (infinitivo por ser verbo nominalizado)
+-> artículo nominalizador (facultativo)
So when we get to the second one, we can break it down in the same way
del ser conocida (___)
| | | |
| | | +-> sujeto implícito «esencia»
| | +-> participio pasado (concuerda con el sujeto implícito)
| +-> objeto de la preposición (infinitivo por ser verbo nominalizado)
+-> preposición más artículo nominalizador («de» valdría igual)
While this is perfectly grammatically correct, it sounds absolutely awful for one small reason: ser is also a noun, and in particular, it's a masculine noun, which makes seeing a feminine adjective after it a bit odd. The addition of (a) the explicit subject, and (b) the agent in the first use, help prevent this interpretation and it sounds okay. The second time, though, there is nothing to prevent the reading as "the known being" (rather than "being known"), except for the gender which then just makes it sound wrong, even if, as shown, it's technically correct.
