So I have continued my exploration of how to get the best bang for my buck with regards to battlemats. Here is what I found.
Flip-Mats from Paizo
For portability, I still can't beat the Blank Flip-Mat from Paizo. Given its cost, I can just buy another one. This gives me the ability to recreate any map a pre-printed adventure throws at me and if I take my time in drawing it (before the game), I can do some moderately evocative line art. Otherwise I can buckle down and buy more of their pre-printed flip mats for better presentation (at least for fantasy settings).
Pros: They travel better than Chessex Vinyl maps, if I do need to make some specific counters using static cling vinyls, they will stick very well to the surface. Also I can conquer the fold and "lay flat" issues at home by putting a clear acrylic sheet over the map.
Cons: They can warp over time and don't always lay flat when I travel. However those problems are minor and can be overcome for home games.
Home Made Maps
Since I won't always be constrained by modules, and because there aren't a lot of sci-fi maps out there, I'll make semi-generic, re-useable maps. Common battlefields that I can use such as a cargo bay map, maybe two or three battle station section maps , and just tailor my adventures to these locations. The hard part will be to either price out how much the large prints will cost me, or work out how to make these into my own flip mats using card stock, some sort of thin mounting board, and some permanent con-tac paper (it seems all the stuff at Staples is low tack so it keeps peeling back up).
Pros: Art! Also I can pack up scene maps that I might need for a specific adventure. Once I have a map made, I may not need to make the same location again (unless I feel the map is getting too boring). When I am done with a map, I can share! Plus if I make decorations on static vinyl, then I can get a lot of mileage out of a basic floor plan by using the decorations to change what each room is used for.
Cons: Art! It will take time for me to make my own maps so if the players go somewhere that I don't have a map for, I will have to rely on the blank Paizo Flip-Mat.
In theory they are cool but building a scene with tiles takes time. It takes less time to draw it. And if you aren't adding decorations (which means more tiles) you might as well just use a mat.
Pros: Modular, but not that modular really. At least you can put down the visible elements so the your players have no idea what the full layout looks like.
Cons: Takes time to put together. Too many fiddly bits to manage at an away game. Potentially may eat up a lot of travel space in your kit.