To my knowledge, this is always how deletion of spam-flagged posts has worked. If a post is flagged as spam or offensive and is deleted by a moderator or by community votes (10k, 20k, or review), the harsher penalties are not applied. The post content should still be obscured when seen by 10k+ users later, but the IP-level blocks and 100-point penalties are not applied as a result of this.
The harsher penalties are only activated when the post has been destroyed as a result of 6 community spam / offensive flags or one moderator-applied flag.
I think there are good reasons for this. I've frequently seen misapplied spam and offensive flags on Stack Overflow on content that was later deleted by 10k+ users or in review. These flags are validated on deletion, but were the penalties to be applied automatically a lot of damage could be done by mistaken flaggers.
I'll often use deletion on something that's spam-flagged when the content is somewhat spammy (I don't want to dispute or decline the flag), but I can see that the user behind it might be reasoned with. Applying a 100-point penalty and IP limits would generally prevent any chance of them being able to come back from this.
I can see an argument to be made for spam / offensive flags hanging on after a post has been deleted, for moderators to look into things and maybe clean up after a spammer. I just wanted to point out that automatically applying the spam penalties on a normal deletion would lead to problems.