First of all thanks for the replies, I find this issue really frustrating but so far I can only attribute it to being a bug within thermal expansion of the tekkit pack rather than an issue with the mechanics. I actually figured it out - the tank at the top when it loses a few points of lava (500 or so - the crucible sends the whole bucket (1000mb to refill it) regardless of how much it actually needs.
It is definitely energy efficient, considering netherrack is easy to come by, although while being energy efficient, it is definitely not energy abundant. Here's the math:
To clarify - machine produces an excess of lava over what is used. Otherwise I would never fill up all the tanks with lava (Including the dynamos).
All 5 of my magmatic dynamos have 4000/4000 fuel. They produce 80 RF/t or 1600 RF per second each. 1 bucket (1000Mb) provides 180000RF for single dynamo, now how much does it provide for 5? (At 80Rf per tick and 1600RF per second - in order for all 5 magmatic dynamos to consume 1 bucket of lava (200mb each) it means they have to use up 180k/5=36k energy each. In other words at 1600rf per second: 36k/1.6k=22.5 seconds of work each until they need new bucket). Magma Crucible consumes exactly that amount (Which is why my hardened energy cell which was at 1.9 million when I turned on magmatic crucible - stays there pretty much forever while magmatic crucible works) Just to clarify: 180k in 22.5 seconds is 400rf/tick which is what my crucible eats.
My lava tank has 48000 MB capacity or 48 buckets. 1 Netherrack equals to 1 bucket of lava. It takes 20 seconds for crucible to melt 1 netherrack - producing 1 bucket. It consumes 160000 energy doing so. (wiki says 120k, although at 400 per tick, and 8000 per second - 20 seconds is 160000 RF so there is a problem with a wiki as well? Or may be I'm looking at a wrong wiki) Considering that 5 dynamos produce 180000 Rf per bucket in 22.5 seconds - while not ideal the trade off is clearly visible. there is about extra 125mb every 22.5 seconds (1000mb / 20 * 2.5 extra time = 125mb)
Now I hoped that the 400rf per tick eating machine (crucible) would just stop after all the tanks are filled, so I can efficiently use my millions of RF. But obviously the machine itself decides to waste extra 50-80% of lava to refill the final bucket worth of storage.