I was lucky enough to have airline miles to use, so I dodged the risk-vs-cost question on my June 15 outbound flight (have done nothing about the return yet, but should). I booked a bunch of refundable hotels over the last two or three weeks; I usually play things a lot more by ear, but most of my destinations on this trip are high-cost, so it's risky to leave accommodations until the last minute.
My itinerary includes two overnight ferry trips requiring cabins. Those ferries run only once a day and not every day of the week, so I've had to book those (tickets changeable but not refundable, alas).
I am stubbornly holding off on train tickets (despite having two legs with pinned-down dates and times) and two intra-European flights (both uncertain as to date and/or point of origin). Dallying on those transportation links is going to cost me, but perhaps not as much as I'd lose if I had to reschedule the trip after buying the tickets.
It's been decades since my most recent trip to Portugal, but I don't remember reading here about full trains, and I believe Portuguese trains are relatively inexpensive. I'd work on the hotels (refundable rooms) and the flights now.
Don't assume that all airlines have the same refund/change policy. If you have multiple airline options, take the time to go far enough into the purchase process with each one to be able to see the refund/change policy.