There's the Map Vector Crop tool, it'll let you drag a box around the features you want to keep and removes everything else. Also, MAPublisher 8.3 offers spatial selections, so you can select all features from layer A that fall within the feature(s) on layer B. That won't intersect, only select, but it'll still help you a lot.
I use the Map Vector Crop to clip map layers to the frame extent frequently but for clipping to smaller boundaries inside the frame I prefer the neat results of an intersect. I'm surprised Avneza doesn't have this in MApub. Maybe as a future development.
I have so far had little success using the spatial selections tools in MAPub but I'm sure thats because I haven't read the "how to" yet. This may be a better way to reduce the layer size before using a mask.
Or I can Intersect the data on Monday when I get back to the office. This is probably the most frequent use I have for ArcGIS in my freelance work, I really wish I could do it in Illy.