The engine producer claims that fuel additives should not be present in fuel on their engines with electronic controlled fuel pumps. Is this just a precausion due to no experience (bad or good), or is there a technical explanation to why not?

Any comments?

Each fuel sold in Europe has fuel additives, and you better not use fuel without those additives. What the engine manufacturer means ist that you should not add in addition any aftermarket additives.

Using wrong additives may reduce the lubricity of the fuel, which is bad because the wear of the fuel pump will increase due to the fact that fuel pump is lubed with fuel.

I don't aggre with broad statements like that. The fuel here is so bad that when I didn't use an aftermarket additive I had to rebuild injector pumps every 30,000 kilometers or so. With an aftermarket additive in every tank, I now have one diesel pickup that had had 4 rebuilds in 2 years with not a single problem in the last 480,000 kilometers with the additive. Another truck that had several rebuilds now has more than 200,000 km without a rebuild. My 95 diesel 4Runner had a rebuild at 110,000 before I started using the additive. It now has 300,000 km with no more repairs. My 99 Turbo-diesel 4Runner has 72,000 km on it, using the additive since it had 16,000. No repairs.
This additive elimiates black smoke, gets better mileage, better cold weather starts,etc.

I have two diesel vehicles, one with over 280,000km and never needed injector or IP service and this is in India, where fuel, especially diesel is of dubious quality. I solely depend on DALF from ELF and the newly launched additive diesels which work out very good.