All the above said...
My colleague (now left the job) once asked me if common rail pump timing was necessary when changing timing belts, and I said I don't really know but as its a compressor that generates fuel pressure, I'm lead to believe they are like a rotary compressor that just build up pressure, it may not be necessary to time them I don't know!
I've never until recently carried out any investigations regarding issues with valve timing, however, two things I've come across recently I'd like to share...
1 / The crankshaft sprocket when using a woodruff key I've seen the sprocket to have side to side play in it knocking on each side of the woodruff key!
Back in my day that would have caused me to look deeper into a problem. On this occassion I removed the sprocket and examined it, seeing nothing obvious, however, because I like measuring components I decided to use a vernier and check the diameter of the sprocket at various points around the circumference. This idea is not new to me but was introduced to me back in the 1980's. I never found a fault previously and most of the time didn't get the vernier out, however yesterday I checked a sprocket and behold the sprocket had gone excentric.
For now I can only put this down to the high forces passing through the valve train mechanism from areas such as the diesel compression compressor pump of common rail systems being somewhat extremely high working pressures, and the pumping action over time is distorting the sprockets. understanding this now suggests to me that the compressors should be locked into a set position when changing timing belts/chains.
maybe its time thesedays to change all components of a timing belt/chain mechanism when replacement is necessary!
I tend to rely on service information if the pump needs to be phased. That being said there may be added load to the drive belt or chain in certain positions. It's not an issue I am aware of but an out of phase pump could cause an issue at high mileage that the manufacture is not aware of or is not concerned about.
If a vehicle does not have a phasing procedure, there are ways to align the pump before installing to align the pulses with cylinder TDC. I just don't know what setting would cause the least stress on timing chain/belt components. I possibly would be to look at a newer generation of the engine to see if there is a phasing procedure in the service information. A good example is the 5.9L Cummins is not phased but a 6.7L Cummins is. These are very similar engines and a slight ticking noise can be noticed on a 5.9L and the fix can be phasing the pump even though there is no service procedure for this.
On VW PD engines, crankshaft sprocket is excentric as cambelt elongates during pump unit actuation.
There are some different strategies out there like the 2019-20 RAM 6.7L where a CP4 is run at 1.5 times crankshaft speed to align every second pulse.
I have attached an example of the pulses from a CP3 pump. This is a known good pump. If one or more of the pulses are missing at higher pressure, the output of the pump is reduced. This is a great diagnostic test.