I'm developing a template that uses a random header image. I would like to watermaker these header images, only when images are shown in the header they should be watermarked.

I would suggest to add an additional parameter to 'getCustomImage' that determines if the image return is watermarked or not.

I managed to achieve watermarking selective images by hacking 'functions-image.php', but this is not a sustainable solution...

perhaps you should read the function guide to see what parameters already exist and what they do.