As whoever was interfacing with Inkscape at a low level such document's internal numbers was obliged to be aware and use the old fixed 90 DPI convention, I assume that leaving all numbers at 90 DPI would make the transition transparent for them. Surely they will not be able to use the new 96 DPI convention together with the old one, but this is another problem they'll have to solve by themselves. I suppose that such kind of users will choose not to convert any of their old documents if they don't want to/can't upgrade their external programs. All "normal" users are not going to care much about which numbers are internally stored inside the documents and will only see the effects on canvas: for them there should be no change at all because they are not going to have the knowledge required to fix conversion problems by themselves.
The main purpose of "fixing" the 90/96 DPI incompatibility should be to make "normal" users able to open an old document and keep working on it without the need of further manipulations. I won't mix addressing direct XML edits with normal on canvas usage.
IMHO a much better general approach could be abandoning targeting only the 90->96 conversion and trying to deal directly with the current document unit. That is, if the document is in mm all internal numbers should be moved to mm and the view box adjusted consequently, just like if the document was generated from the new mm template (using mm as an example, of course). My opinion is that "normal" users expect to have numbers in a mm document internally stored ad mm, so this approach should be fine for them.
A similar unit transformation utility may be useful also in other situations as it could be a general tool that permits a deep conversion of document's internal numbers from a unit system to another. I think about it being used on purpose by the user, specifying from which unit to which other to convert without relying on the document's internal stored state (probably a few options about how to deal with special objects like font sizes or filters' parameters may be appropriate). This general utility could be called at a document's opening if the 90/96 mismatch is detected, proposing to convert the old document from 90 DPI to a new unit system (e.g. mm or 96 DPI) and asking the user to specify to which one (proposing the current document's unit for all those who can't really understand what are being asked for and will just press 'Ok').
Luca
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