Assume for a second that the IFHS estimate of 150,000 total violent deaths for March 2003 through June 2006 is correct. How does that gibe with the 50,000 civilian violent deaths as reported by IBC? (Actually numbers are 151,000 for IFHS and 48,000 for IBC, but I am rounding with abandon.) Both are, obviously, much lower than the 600,000 estimate from L2. (Since there were almost no pre-war violent deaths in L2, "violent deaths" and "excess violent deaths" are the virtually identical in L2.) IFHS is 1/4 L2 and IBC is 1/3 IFHS.
First, the US military was killing, during the invasion, thousands of Iraqi troops and, after the invasion, thousands of insurgents. Those numbers are counted in the IFHS total but not by IBC. Donald Johnson points out this article which reports that the US military claims that it killed 19,000 insurgents from June 2003 through September 2007. Guestimating from their table, it seems like the toll up to June 2006 might be 13,000. But this does not include Iraqi military deaths for the invasion itself. Skimming this Wikipedia article, 10,000 seems a reasonable estimate. So, rounding up, we might have about 25,000 Iraqi soldiers and insurgents killed by US forces during this period. I do not have a sense of whether this is more likely an overestimate or an underestimate.
Second, insurgents were killing many non-civilians in the Iraqi population. The deaths of Iraqi soldiers are not counted by IBC but are included in IFHS. I think that the same is true for police officers. Anyway, it is certainly the case that thousands of Iraqi combatants have died, presumably somewhere between US combat deaths around 2,000 and insurgent deaths of 13,000. Call it 5,000.
Third, there has been a great deal of insurgent/insurgent violence. That is what happens when a civil war starts. Some of these are clearly "civilian deaths." When the local Sadr militia picks up a Sunni man minding his own business and kills him, that is clearly a non-combatant death and should be counted by IBC. But when two armed groups are fighting, as in much of the intra-Shia violence, it is not clear if those deaths are counted (by IBC) as civilian or if they should be. Could there be another 20,000 such deaths? Sure.
So, we have 30,000 Iraqi military/insurgent deaths caused by the US military plus 20,000 Iraqi deaths involving combatants in the civil war. (Again, I don't put any particular faith in these numbers and haven't look closely for good data. The point is that there are certainly tens of thousands of deaths, at a minimum, that are included in IFHS but are, by definition, excluded from IBC.
In summary, there are 50,000 IBC civilian deaths plus 50,000 soldier/insurgent/combatant deaths yielding 100,000 total. But this is 50,000 less than IFHS. Fine. I don't see that discrepancy as a big one. Could IBC be off by a factor of 2? Sure! Could IBC be correct but my summary of Iraqi combatant deaths be off by a factor of 2? Sure!
In general, the IBC and IFHS numbers are broadly consistent (as both the IFHS and OBC principal investigators would no doubt agree) because IBC is counting a subset of the deaths captured by IFHS.