This is common to just about all DVD/HDD recorders, I imagine: certainly all the ones I've personally used. They are largely automated, and we don't have very fine manual control over the authoring process. So, we cannot dub scenes of less than two seconds because the automated authoring always takes into account the 1/2 to 1 second margin of error needed to ensure cleanly transferred edits that adhere to the compatible "finalized" DVD Video standard.
It is highly unusual to need such brief edits on a DVD/HDD recorder: if you often do projects that require many such short segments, you really must look into PC-based DVD editing/authoring software. The PC allows manual control of very brief edits, because it will encode the entire project file to flow smoothly before you burn it. You would have more flexibility in cutting if you record the videos directly onto the PC as AVI files, and edit in AVI format before creating a DVD, instead of trying to edit the MPEG2 DVD files. But the better DVD authoring packages should let you cut very briefly even with DVD files ripped from your Pioneer DVDs. Depending on the software, either the entire Pioneer DVD will be re-encoded (losing some quality), or just the edit points around any shortened scenes.
DVD+RW and DVD-RAM media use a different video edit standard than the older traditional "finalized" DVD/DVD-R/DVD-RW/DVD+R discs. They might allow the extremely tight clip editing during transfer from Pioneer HDD that you want to do. But the resulting discs would only play on hardware that supports DVD+RW or DVD-RAM. You could rip this type of disc to a PC and use the PC to convert it back into an ordinary DVD-R, which might be easier than re-authoring a DVD-R to shorten the edits.