Well, this is not a voukoder bug or issue, but ... Ok.
I don't see any correlation between the spikes and the projects timeline. The project itself is rather simple and uses not many effects and special transitions. I guess it is either premiere or the system itself.
I noticed you are using Bandicam for recording your screen to mp4 (NVENC). I did the same for game recording a loooong while ago (I love bandicam for screen recording). Did you ever try to record to AVI using the MagicYUV codec? It is designed to be mathematically lossless and extreme fast encoding and decoding. I loved working with that. Would be interesting to see if there is any difference. H264 was not designed to be an intermediate codec.