We are talking about transporting tons of equipment trough light years of radiation many times stronger then the one that is already frying computers in satellites and probes within heliosphere, heck even on Earth's surface it's enough to flip bits in RAM dies.

Your original post postulated a species who has solved that which for us, with our known physics, is unsolvable, that being faster than light travel and/or very near light speed travel.

And yet, with such incredible technical knowledge far beyond what our present day knowledge tells us you discount that this same species has not already solved the radiation shielding problem?

By the time your fictional species has solved the FTL problem, they are likely many decades/centuries past having already solved the radiation shielding problem.