You can do this in Bias Peak.
What you want to do is create a long repeating wave of your watermark that is longer than the lengthiest wave you are going to process. You need to open it in Peak, then do cmd-a and cmd-c to copy the entire contents to the clipboard. Then go to the Batch Processor from the file menu. Click 'add' at the left hand side, and open it's settings at the right and choose a percentage mix, e.g. 10%. Then underneath it, choose 'Apply just to first 100%'. What this will do is mix your clipboard wav only up to 100% of the length of the file being batch processed, so it won't make waves longer or shorter than the input file.
I recommend also dropping a normalize after this process, because if any of your files are already loud, adding 10% to them may cause them to clip. I believe the batch process will be done in 32bits floating point, so you should be able to add the watermark then normalize to contain the audio at a consistent level regardless.
Click the Set button at the bottom to choose output location and file format. Then up top left click on the ON to enable batch processing. When you then press OK bottom right, it goes back to Peak's wave window. From now you can drag and drop any number of source files directly onto the Peak icon in your Dock, and it will automatically batch process the lot and spit out files to your chosen destination.
I tried the above, and it worked fine mixing in 10% of my clipboard file but retaining the length of all input files.
This is what you should see!