Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly defined and evidenced that in bacteria the positively charged residues more commonly were found on the "inside" of a membrane (the cytoplasm rather than the periplasm).
However it seems the field has moved away from the idea of "inside the compartment" to "inside the cytoplasm" as more data became available. In a 2006 review even von Heijne describes some transmembrane helices as abiding to the positive inside rule because their positively charged residues were inside the cytoplasm, although never explicitly backtracks on the original definition. A similar review in 2007 by von Heijne offers a more definitive refinement of the rule, however removes the concept from being applicable to subcellular membranes.
...the loops connecting the helices differ in amino acid composition, depending on whether they face the inside or outside of the cell (the “positive-inside” rule).
We are now faced with an awkward rule that doesn't account for proteins elsewhere in the secretory pathway or in the other organelles. All those proteins are inside the cell.
More recently still large-scale analysis of transmembrane helices from different biological membrane surfaces, Sharpe et al., 2010 and Baeza-Delgado et al., 2013, show the clustering of positive charge being cytosolic rather than discussing it in terms of the inside of the compartment. Both of these papers still say that they corroborate with the positive inside rule.
To me it seems that the definition is somewhat sloppy and can broadly be used to say "inside the cytoplasm", despite publications being reluctant to define the rule clearly. Has the definition ever explicitly been changed, or has the field silently changed what "inside" means? ... Or have I completely misinterpreted something? How do the organelles fit into any of these definitions?