No, I think it works better when two things match, because it makes you that much stronger.
It's different then BG.

i am thinking of the scoundrel/guardian type from kotor 1...
here's my reasoning...(obviously i've not only got the cheat book, but i've done experimenting as well...)
gains:
greater prestige sense...+1 to defense every 5 levels instead of jedi master/sith lord every 8 levels
sneak attack (which becomes the most powerful attack feat in the game when you factor in all the classes have the SAME base attack bonus per level...)
more skills for you
better vitality
MORE FEATS!!! (the jedi watchman and weapon master have the same feat progression table!!!) you can now even afford the precise shot feats, and the two best melee feats, flurry and power attack
losses:
ok, based on dsimpson's guide, if you have light side mastery, and a consular/jedi master, you actually get 6 (3 + 3 ) wisdom points when you get prestige class after light side mastery...the second 3 points don't show up, but its there...now i am thinking that if you change classes, you get 3 to wisdom and 3 to con, for the different class...which is not as good as a 6 to wisdom of a consular/jedi master, but its not terribly bad...
less force points...but better than a consular/weapon master...
loss of lightside enlightenment (that one hurts a lot since you can give jedi handmaiden or jedi atton lightside mastery when you turn them into jedi)
loss of inspire followers (not a big concern as force meditation is better in almost every aspect)
better defense, killer combat ability, for less force points, and some jedi master perks...
really hard to make up my mind...
probably save before choosing and try out both...
but really there are some major bonuses (and of course drawbacks) for either choice...
They call me....
Darth...
Darth Gizka...