It's been a while since I last set up sync on a new iPhone. I created a backup of my Joplin data, and desktop and old iPhone are synced. I deleted the Joplin welcome notes from new iPhone.
All I need to do now is enable encryption, enter the encryption password on new iPhone and let it sync, as well as disable screen timeout (assuming that's still a thing for Joplin sync)? Is that correct?
Everything's correct, good job making the backup 
Sync has been running for nearly 3 hours. I'll have to run some errands soon. Is it ok to interrupt sync by leaving the wifi range, and switching apps? When I come back and sync, will it just pick up where it left off?
yep, it should resume next time
Initial sync took ~3.5 hrs. Subsequent sync (i.e., pressing sync on phone shortly after initial sync completed) has deleted over 1500 remote items so far and still going. Confusing/worrisome, but I vaguely recall there are note history items and this is probably what is being deleted (or trying to delete and may not even be on this new device). I forgot how poor the initial sync experience is with Joplin. Definitely a pain point for new users coming over from Evernote or other note apps.
Joplin Server/Cloud mostly solves this. Which sync target are you using?
I'm using Dropbox. 10,200 "remote items" deleted (over 3 hours now) and still going; and as described earlier, this is after the initial sync showed as complete. I could definitely see a newbie to Joplin, or someone who didn't make a backup just before doing initial sync to a new device, panicking.
Both initial and subsequent sync are on 5Ghz wifi network.
Edit: Finally tally was ~10,700 remote items deleted in almost 4 hours.
Did you happen to set the keep note history for setting, to a large value on your old iphone and desktop client? If that is the case, I suspect it is deleting a large number of note history items because when you set up a new client, the default value is 90 days. So if it's a smaller value than your other clients, there will be some note history deletion.
There are future plans to either expand upon or hide the breakdown by default, of create, update and deletions while syncing, so that you have to expand a section to see that information (which is essentially debugging information)
All 3 Joplin devices - desktop, old phone, new phone were set to 90 day note history.
Is the client on your old iphone and pc an old version / updated just recently? I can't remember the version exactly, but the note history expiry only started working in 3.2.x, so earlier versions wouldn't delete the old note history
desktop: Joplin 3.2.12 (prod, win32)
old phone: 13.2.5 (prod, ios)
To be honest then, I don't know the exact reason why the deletions have only started happening now.
But to confirm that it is actually note history being deleted, can you send the deletion log for the Joplin client on your new iphone? This is available in Configuration, Tools, Deletion logs. Just share that file to yourself, zip it and attach here on a post on the forum