There are a few points that I believe require consideration here. First, the reason they use the RPI and not Massey or Sagarin is because they do not want margin of victory (MOV) included in the ranking they use, as it would encourage teams to run up scores. Thus we need to use rankings such as RPI or ELO Chess that ignore MOV. I guess you could argue whether or not that's a sound reason, but as of now, that is the methodology employed. Baylor is currently 5th in RPI and 4th in ELO Chess while MOV ratings hold them in the highest regard (Massey 2nd, Sagarin 2nd).
Second, Mulkey KNOWS that they use the RPI and that they will penalize you if you play too many hopelessly overmatched teams (cf Maryland 206-17), but she scheduled her murders' row of Lilliputians anyway. Why? Possibly because teams that were ranked a bit higher can request home-and-homes instead of just playing in Waco. Which leads to...
...Third, Baylor will have played 16/29 (55%) games at home this season (11 road 38%, 2 neutral 7%). Miss. St. is similarly bad: 55%, 31% 17%, as is Louisville: 55%, 45%, 0%. . In contrast UConn's numbers are 41%, 45%, 14%. Notre Dame is 45%, 45%, 10%. Creating a quick metric by adding the % home game to .5 x % neutral games, here are the "most homey" schedules of the top 16 teams in RPI (listed by how homey their schedule is):
61.7 Miss. St.
58.6 Baylor
58.6 Duke
58.1 Oregon
56.9 Tennessee
56.9 Mizzou
55.2 UCLA
55.2 Texas
55.0 Ohio St.
54.8 Louisville
53.4 Maryland
53.3 Stanford
50.0 Notre Dame
50.0 Green Bay
48.3 UConn
48.3 Florida St.
This is one list where you wanted to be ranked low, as it means that you play more games in hostile locations. So not only does Baylor have one of the most home dominant schedules of the top teams, but they also play a lot of very bad teams (see point 2 above). That's a double whammy.
Fourth, even if you argue that only games against top teams matter (as you do), Baylor has played fewer top 50 teams than the other top contenders.
Top 50 opponents (counts all games schedule in regular season)
16 Notre Dame
15 Stanford
15 Oregon
15 UCLA
14 UConn
13 Louisville
13 Tennessee
12 Ohio St.
12 Miss St.
12 Florida St.
11 Duke
11 Texas
10 Maryland
9 Mizzou
8 Baylor
5 Green Bay
The eye test suggests that Baylor is excellent, and woe is the team to have them as their 2-seed (if the Baylor fails to be awarded a 1-seed). But didn't many people feel that way about Maryland last season and that didn't work out well for Maryland. I would be disappointed to have Baylor as Notre Dame's 2-seed, but I still think that the Irish could beat them.