First off, some rod makers recommend specific models of line by specific manufacturers. They have designed their rods with this fly line in mind. When that's the case, I strongly suggest that you follow that rod maker's advice. A lot of time & thought went into it, so you're probably going to get the best results if you use the line they specify.
I don't design my rods in this way for a couple of really big reasons. One is that I don't trust the large tackle & fly line manufacturers to keep certain products in production & available. So I'm not going to go through all the hard work & time to design a rod with an exact model of fly line in mind, only to see that line become no longer available someday. Then we'd be left searching for "the next best thing" &/or not getting the most out of the rod. Another reason I don't design a rod to a specific model of line is because everybody casts a rod differently. There are so many variables when designing a rod that all a rod maker can really do is make a rod that meets the criteria for the fishing that the client has described & the way they fish. Make the BEST rod possible for those conditions & everything should be just fine.
So, when someone asks which line to use on their new rod, my answer varies based on the client's situation.
If you're an experienced angler & also keep up on all the latest tackle innovations, etc then I recommend that you use your judgement. You've cast many of the lines on the market, know the difference in how they act, & know you're own casting very well so use what you think is best for you - after you've wiggled the rod some.
If this is you're first custom made rod & you really want to see the difference between the factory-made rod you've been using & the new custom-made rod, then use the same make & model of fly line you've been using (in the correct weight for the new rod). This will truly show you the difference. With so many variables in the mix when it comes to comparing fly rods, using the same line will take away one of those & give you a better comparison between the two rods.
No matter what your situation (if your an experienced rod collector or getting your very first custom rod) I urge you to visit, or find, a local fly shop who's staff you trust. By all means take your new rod (& reel if you like) to the fly shop when looking to buy a new fly line. Show them your set-up & talk to them about the type of fishing you want to do with it. I'm sure any legitimate fly shop folks will be more than happy to work with you to get the best fly line for you onto your reel. Like rod makers, they want you to succeed & enjoy the sport.
As you're getting your gear ready for the upcoming trout season, take a few moment to look over your fly line. Maybe a call to your rod maker & a trip to the local fly shop will be in order.