Mike is correct about setting the saddle into the bridge with glue, it will tighten up any gaps and give the most efficient acoustic energy transfer. However, I’m not so sure using a spark plug file to square up the slot is the best way to accomplish what I am concerned about. Look at this graphic:
In both the top and bottom graphics, they show a nice square slot when viewed from the side (small graphic on the far left). However the top graphic is a properly cut slot, square (from the side) and dead flat along the length of the bottom of the slot. The second graphic shows a slot that is also square (from the side) but is a bit uneven when checked for flat along the length. The gaps are marked in red and represent places the bone saddle is not touching the bottom of the slot.
In the second graphic, quite a bit of energy is lost (along with tone) when compared to the properly cut slot above it. Generally, slots are cut pretty flat along their length when the guitar is first built (usually cut with some sort of router, CNC or Dremel) using a jig that provides an accurate slot depth along the length. However, a poorly cut saddle (uneven along the bottom), sitting in the slot over time, can cause the slot to have low and high points. Also, if the slot was poorly shimmed (to raise the saddle) or a UST as poorly installed, or even the drying of the wood can cause the slot to become uneven along it’s length.
This is very tough to measure as you cannot see the slot bottom if you lay a straight edge in the slot. Also, a short straight edge will not necessarily rock in the slot to show it is uneven.
As Mike mentioned, gluing the saddle into the slot can/will fill these gaps and should increase the quality of the tone IF this is the cause of your tubby tone. If not, then you have just glued your saddle into the slot (not something I recommend as saddles require work and adjustment relatively often).
The other fix is to have the slot leveled along it’s length. This is usually done by using a bridge slotting jig and re-routing the slot to an even depth along it’s length. Obviously, the absolute least amount of material is removed to make the slot flat (between 1/32 and 1/16 inch is usually plenty). And this can be pretty easily checked by examining the slot during the process of routing (some folks will use a light colored marker to mark the bottom of the slot so that when all the marker is removed along the length, you have a flat slot).
As I mentioned above, this is not a particularly common cause for tone loss, however I have seen it several times over the last 40 years and your description of the tone points to this as a possibility. For someone with the bridge slotting jig, this is an easy repair.