Nothing but misunderstanding and fear.
It's the easiest thing, the best method to use, and there should not be 10 posts of replies about something so simple.
Yes, you need to have the exact same halftones and just either:
A) choked back the base dots by a couple pixels at 1200 dpi.
B) trap out the color dots by a couple pixels at 1200 dpi.
No they don't have issues registering it, the dots get trapped great and it works awesome. It's not done in the rip, RIP's are all BS, its simple enough to make halftones in PS and then perform your choke/traps on them. The other way is adjust the curves on the base to have the halftones at same angle actually be in the same posittions but smaller... however the choke/trap works just as well.
It's funny how some of the simplest things are the best solutions to a given problem but nobody knows about it.
See attached... I think I wrote another post about this once before.. but I gotta make videos and just spill my guts about all the stuff I've learned over the years... trying to help in random posts on forums doesn't make a dent.
When you have your greyscale sep of the 1-color gradient...
Image> Size> Upsample to 1200 dpi Nearest Neighbor
Image> Mode> Bitmap / Black and White...
Choose halftone, 1200 dpi, set your angle and dot type (round, 22.5 etc.)... then convert back to greyscale....
You can then select just the white background pixels as a selection, perhaps with magic-wand, zero tolerance, non-contiguous.
Select> Modify> Expand - 1, 2, 3, 4 pixels or so... usually 2 is good enough at 1200 dpi with choking actual halftone dots.
Then with your selection now expanded (the white) -- you fill with WHITE and it cuts back all those dots. Trapping is done by selecting the black instead and expanding then filling with black.
It's not a pain, its really simple, and its easy to print through a 110, 160, etc, 45 LPI, is fine etc. The registration is a piece of cake because the dots are choked. You can fade any ink color into any shirt color with this technique I've done it thousands of times its easy and works great on press even gives you ROOM for mis-registration... not harder to register you've got it backwards.
It's not "high-end" printing to fade halftones or to fade halftones with each other (simulated process) or fade them into the shirt, trap and choke dots or interlock them etc.. The same detail is needed on a screen with lots of lines and thin text as with a halftone screen, its just quality screenmaking with some good tolerance on the dot-response curve and it comes out great. Manual or auto it works the same, you're choking the same halftone dot pattern (or trapping one) and it has forgiveness on-press... comes out much better and doesn't do the ghosting effect you see when people don't pay attention to the underbase dots choked for all colors and black inverted etc.... but I will have to cover this stuff more in-depth in new videos and screenprint training to really get the point across.
People will say everyone has their own way of doing things in screenprint, but unfortunately there really are situations in which there are best-practices that will work out correctly compared to other methods which have more or less room for error or are completely the wrong way. It's not rocket-science but YES it is color science and print engineering.
We are stacking molded-plastic-paint with stipple-techniques over twines of fabric. It only comes down to having the "ink" fall in the right positions relative to each other... trapping/choking dots is not really any harder to print on-press than the trapping/choking of text or other complex shapes.
It's all about having the average-blur effect of seeing the stippling or other details from a typical viewing distance. When the base is generated in rip from the same gradient, and no curves applied... THAT is when they have a hard time registering the exact-dot pattern... so you choke the base dots and perform the rip yourself which is better.. and its simply the right way to fade your ink into your shirt if the ink is not opaque enough to work on its own over the shirt color.
Photoshop and Corel have had the capability to manually make your own halftones for a very long time, going way back... it should be like one of the first things any screenprinter learns to do after just knowing how to pull spot-colors and make those films. Next should be simple halftone learning and how to make your own and control your seps and films better. It's really nothing more than a few steps in either program.