By rightclicking, you can assign custom colors to individual slots, thus also to a row of slots (pattern).
Retaining pattern number is possible too - by default, Renoise is keeping things sorted for you but you can disable this feature - check out our wiki
As for the scrap feature, this is something I have thought about too. Not only because it’s a neat additional feature but because it would make it less likely that you accidentally delete a source for aliased slots.
Check out that discussion here