A blood clot doesn't mean there is no foul play. There are plenty of poisons that cause clotting: https://go.drugbank.com/categories/DBCAT000113 - including some that are snake venom components.

It could also be a consequence of prolonged confinement without much movement. It could also be an eventual consequence of the 2020 poisoning (there is no evidence that Novichok specifically or mild poisoning with other acetylcholinesterase inhibitors causes clots; however, severe poisoning causes respiratory paralysis which causes hypoxia, and that can cause platelet and vascular dysfunction/damage that increases the risk of thrombosis. Not many people ever have been poisoned with Novichok and survived, so the exact sequelae are uncertain).

Now, there is a question of whether the FSB would want to do a subtle execution or an ambiguous one. They did attempt an obvious one in 2020, given it involved an agent which is clearly associated with the Russian government (although perhaps if he hadn't made it overseas, that would have never come out). Since then, perhaps Putin and the FSB have less incentive to be brazen. If they didn't want to send a message, they could have just kept Navalny alive. But maybe ambiguous was a compromise they wanted - it keeps would-be dissidents fearful, but provides the cover of plausible deniability for those who would criticise the killing of a political opponent.