I rebooted and reran build in case this was another funny heisenbug.  It isn't.  Before patch, start 3.6 repository IDLE. Click Options, Configure IDLE, and Keys tab.  Look at 'Use a Custom Key Set'.  It says 'Terry', which is correct.

After patch: repeat. It says 'IDLE Modern Unix'.  Custom Key Binding box reflects change. Repeat with 3.5 repository IDLE: it still says Terry.  Ditto for installed 3.6.0a2. 

My custom [Keys] section: 

[Keys]
default = False
name2 = IDLE Modern Unix
name = Terry

The problem is that name2 should be treated only as default, never as custom, and should be used only if default=True.  This is true in CurrentTheme.  However, your revised CurrentKeys uses it first and unconditionally.  Hence the observed behavior.

CurrentKeys should use the same logic as CurrentTheme.  In fact, the common logic should factored out into a separate function with two or three parameters and used by both.

If, as you claim, CurrentTheme is buggy, it should be fixed before using it as the template for both.  To test and claim that it was future proof, I did something like the following last fall. First set config-main.cfg [Keys] name2 to something non-existent, that might be added in the future.

[Theme]
default = True
name2 = IDLE Future
name = Custom Dark

Then start, for instance, 3.5.2.  The non-existent IDLE Future is ignored and replaced with the default default IDLE Classic, as intended in the code.  No warnings.  What exactly did you do to claim otherwise?

---
Also wrong, even with your patch removed: '()Use a Built-in Key Set' says IDLE Classic Mac (slightly grayed) on all versions. If I select built-in, change built-in selection to IDLE Classic Windows, select custom again, click [OK] to close, and reopen, the unselected built-in has switched back to Mac.  This must be a pre-existing bug that makes Classic Mac the default builtin when custom is selected, This is in spite of config-main.def having 

[Keys]
default= 1
name= IDLE Classic Windows

This, of course, is also wrong on non-Windows, which is why you changed it.  But it is also being ignored when custom is selected.

The problem must be in how configdialog gets the default key set when the current keyset is custom. The widget is a DynOptionMenu, created in CreatePageKeys, line 335, with no content.  The options are set in LoadKeyCfg, lines 1055 and 1069.  The latter is used when the current key is custom.  It sets the grayed out default option to the alphabetically first among default key sets.

            itemList = idleConf.GetSectionList('default', 'keys')
            itemList.sort()
            self.optMenuKeysBuiltin.SetMenu(itemList, itemList[0])

itemList[0] should be replaced by your new system-sensitive idleConf.DefaultKeys().