The manual isn't real clear on the finer points in any of the sections dealing with AEB, is it? Of course if the manual did that with every option on the 5Ds R and how changing one setting affects the behavior of other selected settings it would be very long. The various combinations of options available in just the AF section alone would probably take up thousands of pages!
To get exact details for any particular scenario with regard to exposure mode, ISO, aperture, and shutter speed selected as well as other options that allow shifting those values when needed with AEB you're just going to have to play around the camera/lens in question. There are just way too many permutations to cover them all in the manual or in an answer here.
I don't have a 5Ds R, but I checked my 5D Mark III. Since the specifications with regard to AEB listed by Canon are identical for the two cameras I would be very surprised if there was any difference between the overall way AEB is implemented on these two models. It will allow setting a full 3 stops between each bracketed exposure, even when 7 bracketed frames are selected for a total of 18 stops difference! [Total number of stops is (n-1) x i = S where n is the number of frames, i is the interval in stops between each frame, and S is the total difference in stops between the darkest and brightest exposure.] How this works out practically will depend upon a plethora of other settings selected by the user. Among them will be settings such as Safety Shift (Tv/Av or ISO), Auto ISO, and Maximum ISO allowed with Auto ISO.
Obviously, if one is shooting in M or Tv mode and has a shutter speed selected that is less than 9 stops away from the minimum (1/8000) or maximum (30s) Tv of the camera's capability, either the Av or ISO or both must also be enabled to shift to effect the full bracketing sequence. The same is true of the Av setting - if one is already within a stop or two of the lens' maximum or minimum Av setting, ISO or Tv or both will also have to be allowed to shift for an accurate full sequence to be allowed.
(Seven frames at 3EV intervals and bracketing sequence set at -,0,+ for the following examples)
Example 1: I set the camera in M exposure mode, selected ISO 400, f/7.1 and 1/15 second. The seven frame sequence all used ISO 400 and f/7.1. The shutter speeds were 1/8000, 1/1000, 1/125, 1/15, 1/2, 4", and 30". (The selected shutter speed of 1/15 was intentionally selected as it is the only one available that allowed for 9 stops latitude in both directions.)
Example 2: I set the camera in M exposure mode, selected ISO 400, f/7.1, and 1/500 second. Because Auto ISO and Safety Shift were not enabled, the seven frame sequence all used ISO 400 and f/7.1. The shutter speeds were 1/8000, 1/8000, 1/4000, 1/500, 1/60, 1/8, and 1". As you can see, the required Tv for the first two shots (1/256,000 and 1/32,000) were out of range so the camera used the closest setting available (1/8000) for each of the out of range shots.
Example 3: I set the camera in Av exposure mode, selected ISO 400, f/5.6. Safety Shift was set to Tv/Av enabled. The camera was pointed at a mostly white object in an indoor setting lit by two 13W CFL bulbs in track lighting type hoods aimed at the subject. ISO 400 was used for the entire seven frame sequence. The Tv-Av combinations used were 1/1000-5.6, 1/125-5.6, 1/15-5.6, 1/2-5.6, 4"-5.6, 30"-5.6, 30"-2.8. As you can see, the last frame should have been f/2, but that was out of range for the maximum f/2.8 aperture of the lens being used so the camera used the widest Av and slowest Tv available. You could manually shoot a frame for 240 seconds (3 minutes) at f/5.6 using the Bulb setting, but the camera will not exceed 30" automatically.
Example 4: I set the camera in Av exposure mode, selected ISO 400, f/5.6. Safety Shift was set to ISO enabled. The camera was pointed at a mostly white object in an indoor setting lit by two 13W CFL bulbs in track lighting type hoods aimed at the subject. The Tv-Av-ISO combinations used were 1/3200-5.6-400, 1/400-5.6-400, 1/50-5.6-400, 1/6-5.6-400, 1.3"-5.6-400, 10"-5.6-400, 25"-5.6-1250. As you can see, ISO 400 and f/5.6 were maintained throughout the sequence save the last frame, when ISO was shifted to 1250. Interesting that it chose 25" and ISO 1250 rather than 30" and ISO 1000.