Understanding とは in this sentence

Question

Maruko's cousin is charging her money for dealing with her dead pets. When Maruko complains about an aditional charge he says:

「あたりまえだ。さっきのは生きてるか死んでるか確認するためにもらったお金だろ。死がいの穴埋めとは別だぞ。」
Of course. I got money just now for checking whether they were alive or dead, right? ****

I can't understand 死がいの穴埋めとは別**だ.

Despite the dictionary definition of 穴埋め (stopgap) I'm assuming its just a compound of 穴 and 埋め meaning 'burial hole'?

別 presumably indicates 'additional/separate', referring to the charge for the service?

Assuming I've got these parts right the bit I really don't understand is とは. I know two uses of とは. One is to define something, the other is to express surprise. Neither seems to fit here. It could just be two separate particles but then I don't understand the function of と if this is the case.

Overall I think I should translate as

(digging) a grave for the bodies will (cost) extra.

Answer 1

「あたりまえだ。さっきのは生{い}きてるか死{し}んでるか確認{かくにん}するためにもらったお金{かね}だろ。死{し}がいの穴埋{あなう}めとは別{べつ}だぞ。」

In the last sentence above, its subject is unmentioned. If one thought 「死がいの穴埋め (the burying of the dead)」 was the subject, one would forever be lost in one's comprehension of the sentence.

The subject is unmentioned and the predicate is 「別だぞ」. What is the subject, then? It is mentioned in the preceding sentence (as usual). It is 「さっきもらったお金」. Trust me, this is the prerequisite for any analysis of the sentence. That could not be emphasized enough.

「と」 is your go-to particle for saying "different from", "a separate matter from", "same as", etc. If you remember anything from my answer this time, let it be this as you need to know it as long as you study Japanese.

「は」 is attached for emphasis.　The main particle here is 「と」.

The sentence is saying "(The money I received a while back) is a separate matter from (the money I should receive for) 死がいの穴埋め".

Despite the dictionary definition of 穴埋め (stopgap) I'm assuming its just a compound of 穴 and 埋め meaning 'burial hole'?

Exactly. It refers to the burying of the dead. In other words, the word is used for its literal meaning. "Stopgap" is its figurative meaning.

別 presumably indicates 'additional/separate', referring to the charge for the service?

Precisely.

Your interpretation "(digging) a grave for the bodies will (cost) extra." shows your understanding of the sentence.

Example:「イギリスの紅茶{こうちゃ}は、日本の緑茶{りょくちゃ}とはかなり味{あじ}が違{ちが}う。」 ("English black tea tastes quite different from Japanese green tea.")

「とは」 can be replaced by just 「と」 if there is no need for emphasis. Again, it cannot be replaced by 「は」 because the subject of the sentence is 「イギリスの紅茶」.

Answer 2

Myself, I tend to think of ～とは as "as for ~". However, you can probably just interpret it as the "quoting と" + "topical は". I.e.

"死がいの穴埋め"と

when talking about burying the dead bodies...

は別だぞ

... [it is] a separate matter

BTW, EDICT has an entry for とは別に:

とは別に 【べつに】 (adv) in addition to; apart from