Lithium thionyl chloride has a much flatter discharge curve than Li-ion. Here's the discharge graph of a Varta C size 8.5Ah LTC cell:-
and here's a discharge test of an LG 2600mAh 18650 Li-ion cell (a 5.2Ah battery would use two of these in parallel):-
Both types maintain over 3.4V until ~90% discharged. The Li-ion cell starts at much higher voltage so it could deliver more Watt-hours than an LTC cell of the same capacity. however to take advantage of this extra energy you would need to use a switching regulator to efficiently drop the voltage to 3.3V. If you use a linear regulator it will simply waste it as heat.
So the LTC cell's higher capacity for the same size probably makes it a winner, provided the GPS tracker never draws much more than 10mA. If it draws ~40mA or higher when active then you could have a problem, because the LTC cell's voltage drops to ~3.4V at this current. On the other hand the lowest current the LG Li-ion cell was tested at was 200mA (which equals 400mA for a 2 cell pack) so it would have no problem supplying over 40mA peak current.
Li-ion cells have another major feature that may be useful - they are rechargeable. If the LTC cell needs to be replaced more than a few times over the product's life cycle then a Li-ion battery may be more cost-effective and convenient. However a Li-ion cell will be damaged if allowed to discharge below ~2.7V, so you would need a way to disconnect it when discharged - eg. add a Protection Circuit Module (PCM), or buy a pack with one built in.