Actually it's quite lossy with cobble. The only thing that is 1:1 is netherrack at the moment. And yes, both geothermals and magmatics need a bit of a balance pass - I have it on pretty good authority that magmatics are getting one, so I would not rely too much on them.
They'll still be useful, but there's a somewhat incorrect perception that they're by far the best engine right now. Unfortunately, perception is everything (even if wrong), so they get a nerf to wake people up.
Nooo not my beloved magmatics
.. they are quite awesome when used as you likely originally intended. But I honestly don't mind a tweak there as I tend to move to boilers as soon as I have the resources. It's really the geotherm that's tossing conversion out of whack at the moment.
Can Railcraft boilers take BC energy?
Boilers create BC energy, burning fuel (solid or liquid) to heat water and generate steam, which drives steam engines. Up to 18 commercial steam engines per full-sized High Pressure boiler (9 commercials on a full-sized Low Pressure boiler). That's 144MJ/t and 72MJ/t, respectively. The reason that was brought up is because it is often the source of excess BC which is a good candidate for EU conversion. If you already have excess BC stored, say, in a redstone cell that you are looking to convert, then that option doesn't directly apply (neither do the bio/petrol gennys for that matter).
You are back to using that stored BC energy to create fuel to generate EU (whether through a refinery, farm, etc), which is what you are doing with the Crucible - the only difference (besides current conversion rates) is which energy net the generator is sitting on. BCs EU generators control the conversion loss well. IC's Geotherms, accepting a universal fuel, weren't necessarily designed with the current situation in mind, which is trucking lava and its elegant contemporary, netherrack, back across dimensions as a nearly limitless resource.
If the Crucible created "Lava Goo" which couldn't be processed by the Geotherm without a BC-controlled lossy conversion, it still wouldn't matter - because lava pumps / bottlers / ender chests / mystcraft etc. The Crucible actually solves the liquid laghell caused by that scenario.