I wanted to ask if there's a way of defining when a watermark appears. For many projects clients want a watermark for a period of time but not right until the end. Is there a way of defining in and out points?
Not with the Image Overlay effect that you can apply in the Export Media window. You'll have to do that manually with a separate layer over your video inside of Premiere or After Effects.
You can file a feature request here: https://adobe-video.uservoice.com/forums/911308-media-encoder
Make sure you give specifics for how you'd like to see it work. Also, keep in mind that none of those effects allow you to specify an in/out period, and of course, you couldn't just say "apply to the last 'x%' of my video" because that could be a vastly different result for everyone. Those effects are meant to be applied globally, so it seems out of scope for that feature to work like this, but if enough people vote on your request then it will be considered.