A new paper in Science on biofuel indirect effects indicates significant emissions, and has an interesting perspective on how to treat them:
The CI of fuel was also calculated across three time periods  so as to compare with displaced fossil energy in a LCFS and to identify the GHG allowances that would be required for biofuels in a cap-and-trade program. Previous CI estimates for California gasoline  suggest that values less than ~96 g CO2eq MJ–1 indicate that blending cellulosic biofuels will help lower the carbon intensity of California fuel and therefore contribute to achieving the LCFS. Entries that are higher than 96 g CO2eq MJ–1 would raise the average California fuel carbon intensity and thus be at odds with the LCFS. Therefore, the CI values for case 1 are only favorable for biofuels if the integration period extends into the second half of the century. For case 2, the CI values turn favorable for biofuels over an integration period somewhere between 2030 and 2050. In both cases, the CO2 flux has approached zero by the end of the century when little or no further land conversion is occurring and emissions from decomposition are approximately balancing carbon added to the soil from unharvested components of the vegetation (roots). Although the carbon accounting ends up as a nearly net neutral effect, N2O emissions continue. Annual estimates start high, are variable from year to year because they depend on climate, and generally decline over time.
Variable Case 1 Case 2 Time period 2000–2030 2000–2050 2000–2100 2000–2030 2000–2050 2000–2100 Direct land C 11 27 0 –52 –24 –7 Indirect land C 190 57 7 181 31 1 Fertilizer N2O 29 28 20 30 26 19 Total 229 112 26 158 32 13
One of the perplexing issues for policy analysts has been predicting the dynamics of the CI over different integration periods . If one integrates over a long enough period, biofuels show a substantial greenhouse gas advantage, but over a short period they have a higher CI than fossil fuel . Drawing on previous analyses , we argue that a solution need not be complex and can avoid valuing climate damages by using the immediate (annual) emissions (direct and indirect) for the CI calculation. In other words, CI estimates should not integrate over multiple years but rather simply consider the fuel offset for the policy time period (normally a single year). This becomes evident in case 1. Despite the promise of eventual long-term economic benefits, a substantial penalty—in fact, possibly worse than with gasoline—in the first few decades may render the near-term cost of the carbon debt difficult to overcome in this case.
You can compare the carbon intensities in the table to the indirect emissions considered in California standards, at roughly 30 to 46 gCO2eq/MJ.