Thought/Question. These odd after fab modifications, could they be the result of an assembled jag PCB failing the electrical test QA process (due to tolerances being out in components say) and then these fly-leads/ extra caps are added to rectify these minor faults? IE tying floating inputs high or low, etc?
In 100% of all new units the I would say yes, in used units in 99% of all cases I would say yes as there is always the possibility that the odd used unit will be the result some amateur hacking around trying to do some mod.
It is virtually certain that anything which looks like it was tacked on as an after thought was added to get nonfunctioning/out of spec boards working or correct a post production design error, to just throw a non function board out would be a costly waste if taking a signal from different location or adding a resistor/capacitor can get it working.
Sometimes something as simple as buying the same device made by a different manufacture so as not to halt production can cause problems, as although the function may be the same the specification may not be. For example I designed a circuit around a 741 op-amp from National Semiconductor which worked as expected, however it did not work when I put a Phillips 741 in because despite it being an "equivalent" device its bandwidth was only 800KHz where that of the National (who IIRC developed the 741 in the first place) was 1MHz.
These days you would be less likely to see such things as...
a) manufacturing process have been improved resulting in fewer production errors (i.e. broken tracks) and greater uniformity between PCB's in terms of track thickness and the resulting inter layer and intertrack capacitances
b) PCB design software now includes advanced simulators and design rule checkers that ensure the PCB and Schematic connections match thus ensuring product performance and avoiding any unnoticed wiring errors before the layout is sent for manufacture.
c) Few companies bother to retain service departments as with cheaper manufacturing costs and automated electrical testing it is cheaper to throw bad boards away than to hire people to test & repair them manually.