I realize I was over simplifying when assuming that all the clashes were related to nodumps.
Verifying a 0.88 isn't exactly up to date

> Iirc the clashes are being detected on good dumps only.

Did my trick again and I am not convinced here
For 0.126 I get 40 clashes, but after my trick I only get 30!
So it seems to me that the following 10 are getting a clash on a nodump.

Cloneset: 'boobhack' uses equal names for different ROMs and so it can't be merged to its parentset: 'horekid'
Cloneset: 'catmousa' uses equal names for different ROMs and so it can't be merged to its parentset: 'catnmous'
Cloneset: 'hydrap2'  uses equal names for different ROMs and so it can't be merged to its parentset: 'hydra'
Cloneset: 'omega'    uses equal names for different ROMs and so it can't be merged to its parentset: 'theend'
Cloneset: 'saiyugb1' uses equal names for different ROMs and so it can't be merged to its parentset: 'chinagat'
Cloneset: 'saiyugb2' uses equal names for different ROMs and so it can't be merged to its parentset: 'chinagat'
Cloneset: 'tenkai2b' uses equal names for different ROMs and so it can't be merged to its parentset: 'tenkai'
Cloneset: 'tenkaid'  uses equal names for different ROMs and so it can't be merged to its parentset: 'tenkai'
Cloneset: 'tenkaie'  uses equal names for different ROMs and so it can't be merged to its parentset: 'tenkai'
Cloneset: 'tmekprot' uses equal names for different ROMs and so it can't be merged to its parentset: 'tmek'

With omega/theend you have a simple example of a good rom in parent and a nodump with the same name in clone.
For boobhack/horekid it's actually the case that boobhack is said to use 2 files with the same name, one is good and the other is nodump!