The essence of the deal is it was for the LITR. But you are right there are some complications in how they can use it. Bottom line is they have to be cap compliant when the season starts (and Clarkson would be on the roster) but then they immediately place Clarkson & Horton on LITR.
If you are a masochist or at least have tendencies you can read this and try to understand.
Maple Leafs, LTIR, David Clarkson and everything you need to understand this trade
I haven't double checked this. If you want to waste more time, tell me if this makes sense:
The LTIR benefit comes in in full only if you are hard up against the cap on day one. With Marner unsigned they wouldn't be at the cap, and wouldn't get the full LTIR benefit when they needed to sign him. They needed another LTIR to get to the cap.
Without the Clarkson trade here's the situation (numbers are illustrative, not 100% right):
Cap hit on day one with Marner unsigned - $78.5m.
With Horton put on LTIR, they'd only get $2m in LTIR benefit, not the full $5m LTIR benefit for Horton (benefit is player salary minus day one cap space).
That gives them about $76.5m in cap hit, not enough space left for Marner.
Now with Clarkson:
Cap hit on day one - $81.5m -- Clarkson adds ~$5m and they can subtract a couple million by shuttling ELCs to the AHL for a day.
The next day, get the full LTIR benefit for Clarkson and Horton, and add those couple ELC's back in, and you have a cap hit of $73.5m, a good bit more room to sign Marner.
Apologies if I'm wrong and you just wasted brain cells on this.