Duratio actually kinda adresses this for time instants. If you enter "now" you get an instant. You can move it around the time axis and show its value at a specific zone by using "in zone PST" or similar. So if you enter "now PST" the timezone is considered redundant information and you get an error. But if you say "2013-01-10 PST" it parses. The conversion can be performed by entering "2013-01-10 pst in zone cet".

"today" and similar expressions are calculated in CET. I was considering customizing this or adding syntax for it, but it was de-scoped for the initial release.

I agree, it can be confusing too. At least as long as the "today" is the same on both places, it's clear. I'd keep the full date when it's not today on both places.

And do you prefer the current:

2015-07-13T13:31:47.968+01:00[Europe/Lisbon]

or something simpler?

Yet, the mouse over text for the comic says "ISO 8601 was published on 06/05/88 and most recently amended on 12/01/04."

Is this irony?

Probably not. Nothing is ever irony.