Consider the following bolded sentence from Fate/stay night (previous and next 2 sentences provided for some context).
古来より、魂というものは扱いが難しい。 在るとされ、魔術において必要な要素と言われているが、魂《それ》を確立させた魔術師は一人しかいない程だ。
魂はあくまで“内容を調べるモノ”“器に移し替えるモノ”に留まる。 それを抜き出すだけでは飽きたらず、一つの箇所に集めるという事は理解不能だ。 だって、そんな変換不可能なエネルギーを集めたところで魔術師には使い道がない。
Treating もの as a nominalizer makes it look like "The soul is, at the utmost, something you'd study the substance with [魂は(で)内容を調べるもの], something you'd put inside a vessel [魂は(を)器に移し替えるもの], however this looks quite dubious - can you put the same topic particle は to two different uses in the same sentence? Is there a way to employ は in one way that would make sense in both nominalized clauses?
In other words, I can't make heads or tails with the grammar here. How does this sentence work, and what does it mean?