Premiere pro cs6...3.5 hours of VHS in Mpeg2 i-frame 25 Mbps...Encoding takes 2 hours.I encode to mpeg 2 i-frame
Using FCPX and Apple Compressor on my 2015 iMac 27, I did two test encodes of standard-dev DV material to H264 and to MPEG-2 i-frame at roughly that bit rate.
Encoding 15 min. of content to H264 took 59 seconds; 3.5 hr of content would take 13 min 46 sec.
Encoding 15 min. of content to MPEG-2 i-frame took 1 min 39 sec; 3.5 hr of content would take 23 min 6 sec.
So 2 hr to encode 3.5 hr of similar material does seem a bit long, even for Premiere which is often about 1/4 as fast as FCPX at encoding on the same hardware. I don't know why it's taking that long, but restricting our view to the MPEG-2 conversion times I got, that's a 5.2x difference, roughly what I've observed before when testing Premiere.
Each conversion pathway is unique and can entail varying computational loads and software efficiencies. There are some uncommon ones where Premiere is faster than FCPX. Your best bet is to test various ones and try to find a faster one. If there is some encode setting that CS6 will do sufficiently fast, it might be quicker in the long run to use that then do the final stage of conversion with Handbrake. Or you might find one that is sufficiently fast by itself, even if the codec or bitrate might be different than you prefer.
Another alternative is to simply capture the VHS tape to a file then if trimming is required use a specialized "no encode" tool. It is possible to trim or edit the rendered output file without re-encoding it. You'd have to Google those, but they exist and I've used them before. However test it carefully to ensure it doesn't corrupt the file.
Unfortunately encoding efficiency is rarely documented so it's a matter of trial and error, or asking people with similar hardware/software what their performance is.