I asked in #crystalspace again about possible reasons for rendering problems behind transparent textures. 'mdmkolbe' told me the following:
well you have to make the Z buffer read-only when rendering transparent textures
According to CS docs you make z-buffer read-only by setting z-buffer mode to ztest. Unfortunately, this does not help always (but sometimes it do helps, especially when combined with proper render priority and mixmode alpha).
(and render transparent textures after all the solid textures)
AFAIK there isn't anything like texture priority (maybe binary alpha does it, but it is not acceptable in all cases). CS is object-oriented engine, so if you have model built of both transparent and non-transparent parts you have a problem

.
I don't know how much of the Z buffer stuff CS will take care of for you
That's bad. Who should know it, if developers don't

?
LigH, it seems, that there are two persons which see problems with transparency in CS: You and me

. The rest desperately tries to use what they have

. There are very few entries in history.txt related to transparency handling, there are no bug reports regarding transparency in CS bugtracker, also I couldn't find many (any?) complaints about it on CS forums.
IMO, transparency handling is one of weakest CS features. There are numerous problems related to this:
- incorrectly recognized color formats - try gfxtest application (gfxtest --info imagename) on different images, all PNG's and TGA's are always recognized as 256-color images, TGA's appear to always have alpha channel present. Why walktest and PS work "OK" ? They cleverly initialize one of parameters ("format" property if I am not mistaken) to recognize all images as truecolor images with alpha channel. Strange.
I'm sure that format detection routines don't work properly. - sorting (render priorities) problems - there is no way to define proper order of rendering without using lots of renderpriorities (which now can't be defined in map files); back2front sorting (priority alpha) does not always help.
- visibility culling problems - look at the following simple scene: three cubes and plane with transparent texture (binary alpha set). The plane has attributes: priority alpha and ztest, culler used: dynavis (frustvis it works fine).
[td]The scene

[/td]
[td]Oh! You can't see cubes through transparent texture!

(moving or turning slighgtly makes cubes appear/disappear)[/td]
[/tr][/table]
You can see this effect in PS in numerous places. Let's hope pvsvis will fix it

.
- transparent objects with incorrectly defined parameters tend to behave randomly (sometimes they look better, sometimes worse)
- last, but not least - parts of CS documentation regarding alpha maps are not sufficient, some more info with different, less and more complicated examples, would help map designers.