There is a lot of confusion regarding this issue, hopefully this reply won’t add to it.
There are sever things to consider, what is the deliverable, SD-DVD, HD-DVD/Tape, HDV tape?
Your DP is correct FCP must recalculate [conform] the B and P frames. If for example this was a cuts only project with no effects it only goes through this process once so your not re-encoding for every cut. So in this example you would lose one generation. Obviously HDV is lossy but if this is all you did the difference from the original would be imperceptible. However if you had a lot of cuts it might take a very long time conforming. If your going to master to HDV tape this is probably the best way to go.
If your going to master to DVCProHD it would be better to capture to the DVCProHD codec but this requires an Aja or Black Magic card that can capture analog component. I’m not sure [somebody else will probably speak up to this] whether I would trust making the conversion using batch export from FCP or compressor.
A workflow that will provide much better quality would be to convert to the SheerVideo codec, it is lossless, platform and application agnostic and works well with FCP 5.1.4. Like everything else there’s a trade off. This codec was designed to improve the workflow for uncompressed HD. Using it with HDV will significantly increase the data rate and file size. But if you have enough RAID storage this is a very good alternative to editing HDV natively. I probably wouldn’t choose it for short form work but for long form where you may live with this project for a while I would.
You can check it out here: https://www.bitjazz.com/en/products/sheervideo/
Regarding the Apple Intermediate Codec, again I might use it on some short form work but definitely not on a project where quality was important. It is a 4:2:0 8-bit codec, the only advantage it offers is converting it to a frame based timeline, kinda like big DV. DV is certainly easier to edit but I don’t think people look at it and exclaim, “wow that look great!”
If the JVC BR-HD50 has an SDI out you could always capture uncompressed HD — which is a whole different thread.
I hope this helps.