They Interline the bags. This should not be an issue. Just show your PNR for LIS-MXP-ARN with flight numbers and they'll do it.
I did it once ex-FNC with a TP and LH flights on separate PNR's. bags arrived.
There are 2 separate counters for *G/Business class passengers in Porto. It's opposite the Eco Counters (cannot recall the # of the counters). Go directly there. Saves you a bit of time.
Portugalia (PGA) is 100% owned by Tap. bought in 2008. They only operate TP flights now and have abandoned their NI codes. My opinion, the PGA crews are better although for that flight you'll hardly notice.
The reason for the small difference between one way Y and C is due to the fact one way typically books into Y and B (Tap Plus) , and therefore the difference is quite small to available C/D/Z fares (TP executive).
Seat blocking applies, unless there is a prior Irop or something major.
In Y you get nothing for the 30 min flight. PGA used to give some biscuits.
In C I only flew it once but fell asleep before take off and didn't see if there was service. Don't expect much though. Go for C ticket, think miles :-)
Although the on time record* IME is pretty good, due to the fact you'd be on different PNRs, I would advise to give yourself more time and take the earlier flight.
* - you can check
here today's performance. At the time of writing today all flights had arrived in Lisbon 5-10 minutes in advance (but the wind is in a southernly direction today, making the flight slightly shorter in the OPO-LIS route)
Lounges:
Porto: you can go to the ANA (airport mng company name not all nippon airways

) lounge. Go down the rolling stairs past security, turn left, walk 100 mts, look for the signs for the lounge. go up the stairs. Nothing too fancy. few drinks (go for the Port), some finger food, newspapers. There is a balcony into the main hall of the airport. Can't recall if WiFi is available in the lounge, but if you bring a cable you can connect for free along the airport in Internet posts.
Lisbon: The TP lounge is pretty good. see
here
Avoid the rest of the airport. It needs to be demolished asap.
enjoy Portugal.
GBM
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For future memory the *G counters at OPO are 31/32. Usually only 31 is used.