"Glowmaps work by interpolating the glowmap pixel value with the normal map pixel value."
this is nonsence. if you want to know how glowmapping works I'll explain it, but you don't have this right.
as per your question, (alpha based) transparency works by interpolating the source color (the color of the pixel of the triangle that is about to be drawn) with the destination color (color of the pixel as it is on the screen before you started drawing your current triangle) using the (source) alpha value to weight the interpolation.
you might be wondering still about the visibility issue, well that is a big problem and the only solution that has been found to date is to sort the geometry from furthest to closest ensuring all transparent triangles get drawn without getting killed off by another poly's z value. usually all non-transparent geometry is drawn before the transparent geometry, so the non-transparent geometry does not need to get sorted also. sometimes simply drawing the non-transparent geometry before the transparent geometry is enough, for example if you know you will never (or rarely) have two transparent polys over each other, or if you do that they will somehow still get drawn in furthest to closest order. FSO does not use geometry sorting (currently) but this is the source of the requirement that interiors of transparency enclosed regions (ie cockpits) must be separate child objects to the transparent object (typically the hull) because in FSO child objects are drawn before the parent object, and as long as a child object is completely enclosed by the parent, the child geometry will be further away because of this, and further away needs to be drawn first for transparency.
incedently, the most effecent method for drawing non-transparent objects is closest first, this allows the zbuffer to cull pixels before they are drawn, you will still have the cost of transformation, lighting, and all the other vertex related expenses, but you will save the cost of writeing to a pixel more than once, this is called z culling. it's usually not worth the cost to sort geometry, but if you can get away with it without any/much cost, then you should. unfortunately with (alpha) transparency you have no choice but to go to the expense of sorting your geometry into the worst case scenario in terms of z culling.
there is one exception to the sorted geometry requirement, and that is the case ware you use what is known as 'additive alpha', in additive alpha you do not interpolate based on an alpha value, you simply add the source and destination together, thanks to the communitive property of addition the order in which they are drawn is irrelevant, this is why additive alpha is so popular, the only stipulation is you must still draw the non-transparent geometry first. but unfortunately you can not ever darken (like dark smoke would do) with additive alpha which is why alpha blending is used in spite of it's cost.
this leads to another topic which you might have heard of, BSP trees. a BSP tree allows you to sort geometry in linear time (as opposed to nlogn time). in a BSP tree the geometry of the object is recursively split along a plane (hopefully placed and oriented in such a way as to split the geometry into a half such that there is an approximately equal number of polygons on either side of it). once you have set up the BSP tree all you need to do to sort geometry (furthest to closest) is, at each node recursively visit the furthest node first then the closest, processing a polygon whenever you encounter it (for closest to furthest sorting you just visit the nodes in reverse order). BSP trees can also be used to perform collision detection in logarithmic(!) time, to do this you visit the node which is in front of the split plane first, if there is a collision you will find it in logarithmic time, if you set up your BSP tree so the planes all lie along the principal axises and you put bounding boxes around each node's geometry you will be able to discard roughly one half of the geometry at a time, meaning that logorithmic time is not just a best case but the average and worst case as well.
