Kevin,
This is an interesting problem, and your question and additions communicate the issue well. You are experiencing the "PM Mind Shift". You ask a simple question like "Would material 'A', or 'B' be a better match to this application, and where would I find the better material?". The answers you get range from literal, to "you shouldn't use either A or B", to "You really ought to buy an older DeVere lawnmower off eBay and restore it, not one those new cheap Chinese jobs". Completely off topic.
In that spirit, I offer the following.
My understanding is that the point is to take a 3/4 inch 4140 rod about 10 inches long and stick it into a hole in phenolic 10 inches long, torque it tight, and drill, ream and pin it. The hole is 0.010 oversize, leaving 0.005 on either side?
My thought was that phenolic will deform in the region around the hole long before you get to a torque value anywhere near the bolt strength. So unless there are other factors, I would think you have more design flexibility in choosing the shaft material. "The same strength as the nut" is probably not operative, as the phenolic will fail first (phenolic compressive limit (10% strain) is 36000psi, 4140's yield stress is ~60000psi, if I recall).
The second point is related to the first. If you tighten that bolt at all, the hole is going to distort, right? Is there a valid engineering or marketing reason to have a nice, shiny TG&P shaft for this application? If you are pinning the bolts, this is for relatively permanent installation, right? So the customer never even sees the shaft surface?
I mean, if customers see the surface finish, and it matters enough (as in customers will like the neato finish and are willing to pay more) to up the cost maybe TG&P is worth it. Otherwise, I trust Mr. Addy's suggestion of HR. Worst case, you have a little friction fit which should not be a problem in phenolic, right? And since you are tightening a high-strength steel bolt in plastic, you are willing to accept distortion anyway, right?
Plus, you really should buy an old, American-made lawnmower and restore it. It will last, like 300 years.
J