Yeah, it takes a bit of tinkering, but definitely doable (I think I have Flexify 2). I started with a blank image 2325 x 1100. Once you get your map preset the way you like it, the second button under the axis globle outputs the whole works to a photoshop file with all of the textures as layers (which saves a bunch of time if you're doing several planets). Open up that psd file, hide all of the layers except the 'land color' layer. Duplicate that layer, hide the original, then run Flexify2. Check "Transparent gaps" to get rid of the white background, set input to "Equirectangular", and output to "Icomap". Hit Okay. Then you just need an appropriate hex grid the right size. Here's the one I use (in the gallery, under Maps)
http://www.travellerrpg.com/CotI/Gallery/images/6737/1_IcoHex.png
If your document size is set the same as I listed above, paste it into another layer over the icomap. It should fit with a minimum of fuss, but if needed, scale the size up and down. Make sure you set the scaling constraints on, otherwise the hexes will get distorted. Makes it a fairly simple matter to do things like this
If you use the same process with the hex layer on a much larger map, then you can crop down for detail maps that have the right scale hexes without a lot of hassle.
http://www.travellerrpg.com/CotI/Gallery/images/6737/1_IcoHex.png
If your document size is set the same as I listed above, paste it into another layer over the icomap. It should fit with a minimum of fuss, but if needed, scale the size up and down. Make sure you set the scaling constraints on, otherwise the hexes will get distorted. Makes it a fairly simple matter to do things like this

If you use the same process with the hex layer on a much larger map, then you can crop down for detail maps that have the right scale hexes without a lot of hassle.
