Yes you can do this. There is no problem, from an optical standpoint, doing this.

As mentioned in other answers, polarizers need to be able to rotate to the correct polarization angle in order to be effective.

I own the Lee Filter System, and have done exactly what you are trying to do. It is only a slight hassle to deal with trying to rotate the polarizer behind the filter holder.

If the square filter holder "snaps" on, rather than screws on, to the lens or the filter holder adapter, this is ideal. You can leave the filter holder off the lens, compose your scene, adjust the polarizer, then use a piece of tape (such as gaffer's tape — I always carry gaffer tape in my bag) to keep the polarizer from rotating while I fiddle with the filter holder.

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I also own, and rarely use, a 95 mm in front of the filter holder. From experience, there is actually a very good reason not to use a large CPL in front of the filter holder, and prefer to use a CPL mounted directly onto the lens: there is no possibility of light leak behind a filter that is screwed onto a lens.

With a filter holder, you have to be careful to shield the tops, bottoms, and sides of the filters from stray light entering between the filters. A CPL mounted in front of the stack also suffers from this problem. Every flat glass (or resin) surface in front a lens is a potential reflection problem, and that problem is exacerbated if light can enter from the sides, between or behind filters.

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Finally, there is currently another option on the market. NiSi makes a 100mm × 100mm filter holder that comes with a thin CPL that screws in inside the filter adapter ring, behind the filter stack. The base of the filter holder has a friction thumbwheel to allow you to rotate the CPL mounted inside. The filter is decent, and the holder is nicer (in my opinion) than Cokin's. Also, it comes in a rather nice leather protective box, reminiscent of older photographic lens and camera cases.