I believe you've mixed up or misunderstood a few denture terms. From what you've described I'll assume that your MIL had her lower teeth extracted and the denture put in on the same visit. That would make the denture an immediate denture. When you say "realigned" I believe you mean a soft "reline" which is a hard rubbery filler put on the denture to make them fit better because of the gums shrinking.
As to what is normal practice with dentists and dentures, they all do things differently. They use different procedures that reach the same end. Some charge on a procedure by procedure basis. Some will charge one lump sum for the entire treatment plan. So to answer one of your questions, yes, billing per visit is a normal practice.
Now for the bad news. While treatment plans and costs vary, something is not right concerning the cost of your MIL's treatment. I'll add here that your MIL is not even near the end of her treatment yet. She still has about 4 more months of healing to go through and a new denture or hard relined denture to pay for (if it already isn't included in what she has paid for so far).
Here is approximately what your MIL would have paid for a complete treatment plan for lower dentures had she gone to Affordable Dentures (Binghamton NY fee schedule dated February 2003 and currently on their web site). Her circumstances may have been a little different but I don't think my guess is too far off.
1. initial consultation - $15
2. panoramic xray - $50
3. complex extractions - $90 each x 9 teeth = $810
(simple extractions are only $50 each)
4. temporary immediate full lower "economy" denture = $200
5. Adjustments - assume 4 at $15 = $60
6. Chairside (soft) reline $30 each x 4 relines = $120
7. permanent full lower "premium" denture = $420
(less expensive dentures are "economy" @ $200 or "Custom" @ $325)
Total cost $1675
Affordable Dentures is a discount chain. Personally, I wouldn't go to a discount chain for dentures but their pricing is public and fairly current for comparison purposes. I've used their higher end costs such as complex extractions vs simple extractions, "premium" vs "economy" dentures and all new "final" dentures vs hard relined immediate dentures. Costs at a normal dental practice will likely be higher than Affordable Dentures but shouldn't be anywhere near the $5000 you say your MIL has paid so far. The total cost for full mouth extractions (28-32 teeth) and complete dentures seems to average between $5000 and $6000 in the USA and Canada . Upper or lower dentures separately would be about half ($2500 to $3000). With only 9 extractions (and without any other complications) your MIL shouldn't have paid more than $2500 for lower dentures only.
I hope this information is helpful. If you have any other questions please ask.