In order to answer this question we first have to properly and rigorously define externality. Externalities are often vaguely defined as any effects on third parties but the correct definition of externality is more nuanced.
Mas-Colell Whinston Green (1995) Microeconomic theory states:
"Definition "11.B.1 An externality is present whenever the well-being of a consumer or the production possibilities of a firm are directly affected by the actions of another agent in the economy." .... "When we say 'directly,' we mean to exclude any effects that are mediated by prices.
Mas-Colell Whinston Green (1995) is the most widely used graduate microeconomic text in the world, hence I would consider it authoritative source for a definition of externality. Moreover, most (good) textbooks exclude effects mediated by prices as well (see Mankiw and Taylor (2014) Mankiw (2018) Principles of economics or Cowen & Tabarok Modern Principles of Economics).
Furthermore, your problem is missformulated. Removing congestion from public transport would not be positive externality but reduction in negative externality of consuming public transport (assuming there is any). For example, I do not know of any paper or book that would consider firm that chooses to pollute less (where pollution is negative externality) being positive externality. Reduction in negative externality is reduction in negative externality, not introduction of positive one.
Consequently, in your case the question can be reformulated as:
Is congesting public transport by using it creating negative externality?
Answer is no if we assume that otherwise the market is well functioning and prices are determined by demand and supply. The reason for that is that the negative effect of you congesting public transport by sitting there is already priced in your public transport ticket. So here the external negative effect is already fully internalized in the price of the ticket (assuming no further market failures).
As pointed out in the comments this answer assumes that public transport actually prices its tickets using market prices. I interpreted the question as a hypothetical, but of course in real life it is empirical question if public transport actually uses market prices or not.
Of course, this is not always the case. In some countries public transport is not private, in some it is public-private partnership etc. Also, there is often difference between travelling locally (within city) and more broadly.
A lot of trains in the Europe actually do price their ticket based on the market demand. For example, you can see on the website Omio (price comparison site), that the bus route between Amsterdam and Frankfurt is priced differently on different days (presumably reflecting among other things congestion). You can also see the same for trains here. Hence for these buses and trains any 3rd party effect would be already priced in and there would not be any externality.
However, of course, empirically there are many cities where public transport prices are fixed, or determined not by market forces. In such cases price would clearly not price in the 3rd party effects save for special case where the prices is fixed at what would be market level.
PS: Even if you would not like my reformulation, the above shows that congesting public transport does not create externalities, because whatever the congestion is, it is priced in the the ticket, so by extension claiming you not using it creates positive externality would be a contradiction, given that we already showed in case of public transport the external effects are priced in the ticket.