A train added manually will always generate a valid QR code.
An overview of railway companies where the pass is valid, is here:
https://www.interrail.eu/en/plan-your-trip/tips-and-tricks/trains-europe/railway-companies
More details often on the country pages:
https://www.interrail.eu/en/plan-your-trip/tips-and-tricks/trains-europe/trains-country
Also note that the prices of regular tickets in the Baltic countries are often quite low. A travel day on a pass will often be more expensive.
The ferries between Tallinn and Helsinki only offer discounts and therefore you don't need to use a travel day for them.
In June 23, I travelled in all 3 Baltic states by rail with a digital Global pass, without any difficulties at all. The trains were busy, clean and punctual. In all 3 states - after consulting Google directions, the 3 train companies' apps and local timetables - I added the journeys manually to the Interrail app, and showed the code generated when requested. From Tallinn, I visited Tartu. From Riga, I visited Cēsis and from Vilnius I visited Kaunas. English was spoken at most ticket offices. Using Google Translate, as a backup, I did ask at those train stations with ticket offices about seat reservations but ended up not buying one. Prices for rail journeys in the Baltic States are low. Some, non Interrail tickets can only be bought on the day of use and some are time limited. When travelling between the capitals, I used Flixbus, as the cross border train connections are not yet straightforward. I did not take advantage of the Interrail discounted Helsinki to Tallinn ferry trip, but should have.