Something else is at play here; there should be no difference in how your body cleaves and metabolizes your exogenous Testosterone via IM or SQ.
The reason for SQ, as bass notes very well here, is to increase the number of injections with smaller doses eliminating serum spikes and lowering the risk for increased E2.
There are many things that can effect your free serum levels - like increased SHBG or E2 levels - and I highly doubt it was because you switched to SQ injections.
SQ injections are being recommended by more and more TRT Physicians for all the many benefits.