I started an SVG where I didn't know the size I wanted ahead of time. So I started with the "no borders" template. Partway through, I found transform attributes all over the place. This made my JS code that was going to be inside the SVG more complicated than it had to be. So I spent a lot of time stripping out all those transforms by hand. In most cases, they were just translates.
I would have much preferred to have something in Object/Transform (a new tab) that would change all selected objects and their children such that they no longer need transforms. It would have the options listed below:
*Recurse (turn this off to skip the children of selected objects) -- on by default
*Keep skew information -- on by default
*Keep rotation information -- off by default
*Current layer only (valid only if no object is selected) -- on by default
If no object is selected, the tab would attempt to apply it to the entire file (except as noted in the 4th option, which would prevent other layers from changing).
Does the "Store transformation" from Transforms in Inkscape preferences help? Try the Optimized option.