The only reason why merging targeted tractography with a whole-brain tractogram is suggested in some instances is because for very small pathways, the number of raw streamlines in the whole-brain tractogram may be too small for quantification to be reliable, and so the targeted tracking just boosts the raw reconstruction density in the area of interest. Admittedly I’ve not done exhaustive testing on this approach, and there are potential interactions with the regularisation. If your pathways of interest are reasonably large, it might actually be preferable to not use this approach and just rely on the whole-brain tractogram, if only because it’s a reduced level of complexity and less likely to run into issues at peer review.
There is also a deceptive trap here. When you merge tractograms like this, it’s important that following application of SIFT2, you then select all streamlines belonging to the pathway of interest. This is not equivalent to the set of streamlines generated through targeted tracking: some streamlines within the whole-brain tractogram should also be attributed to your pathway of interest. This applies doubly in your case if you have multiple pathways of interest that “overlap”, i.e. some streamlines should be attributed to both.