I think the onus is on the Corp in these types of scenarios.
The only way for them to be able to go ahead "legally" is to actually confirm with the runner that they don't want to use any paid abilities. If you're running any kind of FA tech, you should be intimately familiar with when someone could clot you (basically always), and need to verify with the runner if you can proceed.
If you don't explicitly confirm, and the runner is clot, they are entirely within their right to say "I was thinking about it, and didn't pass priority yet" after you've tipped your hand. Sure that can be seen as a "rude" play, but so is rushing through the timing structure of a turn without waiting for me. I've had this debate with a few people, and most of them say "well if I give them enough time, that should be fine! I don't want to tip them off to my next move by asking!" and I think everyone who says this is thinking about this interaction the wrong way. This is a huge opportunity for bluff plays, trying to get the runner to commit to spending resources when really it's an NAPD you just dropped on your SanSan. As corp, you need to take ownership of the timing structure and ask the runner if they'd like to react everytime it could potentially matter, which means that when you actually do go for the astro chain when they've got clot, they won't want to burn the 4 SMCing for clot when they could use that 4 to steal the NAPD. Install a new PAD when you've got an astro token scored? Move to play your "shipment from sansan" from hand and pause, asking them if they'd like to react.
For the runner perspective, and from a "play-to-win" mindset:If I wasn't running clot, I'd ask at the start of the game that my opponent be mindful of paid ability windows, which the hope that now they'd always have the threat of clot in the back of their mind, and hopefully play (sub-optimally) around this. Whenever they ask, make a show of considering the boardstate, and ultimately decline to tutor for your clot.
If I was playing clot (which I always do! :P), I wouldn't say anything, and I would hope the corp wouldn't explicitly ask if I was done using paid abilities. After they've tipped their play, the runner is entirely within their right to say "hey, I was still thinking, and never declined to use paid abilities", and then clot. If the corp contests, it really comes down to them having made a mistake (not respecting the timing structure) so judges must side with the runner 100%.
^ There's also the flipside of this, where if a corp knows you are doing this, they can install an NAPD, go to SfSS it, basically baiting you into "interrupting" them, and then advance + icing.
I assume I'll get some flak for playing this way, but I do really believe this is the correct way of doing it. Runners have always had the opportunity to "react" in the timing structure, but only since O&C (hivemind chakana) has it really mattered.
TL;DR: FA is now a bluffing game that both sides need to be mindful of. The rules state that the runner must explicitly be finished using paid abilities before the corp can take their next click. Don't be afraid to use this!