If you are talking about the mask path being visible don't worry, that won't render. Just deselect the layer and you should no longer see the mask path.
If you are talking about some kind of artifact in the alpha channel we need to know a lot more about exactly what you are trying to do and it would really help to see a screenshot with the modified properties layers that you are having trouble shown. You can do this by selecting the problem layers and pressing the U key twice, then dragging a full resolution screenshot into the reply field on this forum or you can use the little camera icon in the tools bar to upload the file.
You can apply pixel poly to a text layer and apply a mask with no problems. You could pre-compose the text layer and then apply pixel poly to the pre-comp and you should still have no problems. If you mask the text layer before you pre-compose you should have no problems. I can't imagine a workflow where applying a mask to a layer that you are going to apply pixel poly to would cause a problem.
Thanks for replying. I'm fairly new to using AE so I went searching for a way to create the effect of cutting out a section of a text layer after another object passes over it, like it's being torn. I came across this video (link below) and followed it in part to get what I wanted.
Here's a couple of screenshots of the end results, showing the modified properties as requested. If you look closely at the screenshot where the layer is deselected you can still see the outline of the mask over the 'SHU'.
Thanks for your time
Click the Expand or Collapse Layer switches panel at the bottom right corner of the timeline so you can see the blend modes. Place the text layer with the inverted mask above the text layer. Change the blend mode of the top layer to Alpha Add. Alpha Add treats anti aliased edge values slightly differently than the Normal blend mode by adding the values instead of averaging them. The line should go away. Apply Pixel Poly to the bottom copy of the text layer.
If you still have problems with the edges then expand the mask on the bottom layer by 1 pixel.