It all makes sense. But a little weird that the story is changing mid-stream. Did he get a wiff of your ignorance about electronics and swap out the good parts? I am optimist and say probably not, he's just giving full disclosure. All those caps he mentioned are better than what came with it, so no biggie. Paper in oil is warm lush (smeared, rolled off) compared to Hovland metal film cap. Orange drops are touted by some modders, but I don't remember their sonic character. You are an engineer, you can swap in anything you like after you get it, if you wanted to experiment.
The resale value of a modded unit is less to a collector. But this doesn't sound like collectors edition anyway, just an old used amp made safe for another 10+ years of enjoyment. If you will USE it then it's a nice piece. If you just want to resell it, then I think you are better off lowering the price of the CDP to sell that quicker. If you think it will sound awesome, forget it, nothing compared to your Naim. Go for Mapleshade if you want modded Scott. Or go for modern design gear if you really want tubes.
Just my opinions. If your heart is set on it, go for it. We'll help you make it work if there's a problem. Any tube tech can fix these small issues if needed. But every fix waters down your Arcam profit, unless you love the Scott, then you have intrinsic value to enjoy.