Translation:He thinks it is good to open the door.
Yes, because he thinks the act of opening the door is good. It's the verb, to open, or to be open, he thinks is good. If it was bona instead of bone, then the sentence would be saying that he thought the door itself was good, something like, "He thinks to open the good door".
In English it's wrong, but in Esperanto it's correct.
In English we don't set apart "that" clauses with commas.
He thinks that opening the door is good.
In Esperanto, for whatever reason, "that" clauses are offset with commas. I don't think Zamenhof was a linguist, and it shows.
In most languages, it is wrong to write a comma directly between the subject and the verb. The only reason for commas between the subject and the verb is if there's an embedded phrase that is being offset with commas, or if the subject contains a comma-separated list. The test is to see if the commas can be replaced with parentheses. If they can, you're fine. If they can't, they might not belong there.
Adam, Sofia, and I went to the party.
I, along with Adam and Sofia, went to the party.
Mi rifuzas meti komon tie. Ĝi estas senutila. Probable, mian opinion influas la franca, kies uzo de la komo mi pensas esti pli logika. Mi pensas ke oni devus uzi ĝin nur kiam oni povus forlasi la tiel apartigata subfrazo sen ŝanĝi la senson de la frazo. Tiel, "mi amas la virinoj, kiu estas belaj" kaj "mi amas la virinoj kiu estas belaj" estus malsamaj.
I agree with you that a comma can make a huge difference between a restrictive clause and a non-restrictive clause. I do not know enough Esperanto to say whether this distinction is handled in a different manner (like with different words) or if it's just an ambiguous mess.
You know enough Esperanto to understand my replies. There aren't really any punctuation rules in Esperanto, unfortunately. If I remember correctly, the Fundamento says it's used "as in national languages" but apparently Zamenhof didn't see that each language uses the comma differently. From the texts I've read, a lot of people use the comma before the "k-" words, but I don't remember ever seeing a comma between the subject and the verb (except for an inserted subphrase). It doesn't look correct for me.
You know enough Esperanto to understand my replies.
No, I just use Google Translate.