A tile with a warp event probably wouldn't have any other kind of event, so they wouldn't necessarily need to stack... but then again, that's delving into the design of an actual quest a bit too far-- there's bound to be some quest designer that would have a perfectly valid reason to do that.
The reason I mentioned them separately is because I'm used to FF6's warps--which come in two flavors: long and short. Short ones are a single tile, and long ones are one tile wide by N tiles long (N being a datum in the struct, with the high bit standing in for a horizontal/vertical flag. Thus, you place it at the upper-left of whichever run you need and give it a width and destination. Those are useful for having a side warp on a map, rather than having 60 little ones.
But, mentioning the event engine, how would events be built up? Would it be a series of scripts that could be called as functions one from another?
I am imagining some essential event commands, such as 'show message x' and 'invoke battle y' and 'move actor A left N spaces'...along with the some flow control to allow conditional execution (really essential for an event engine) and even a call stack for re-use of redundant code in multiple events... Just a few ideas off the top of my head.