I’m not sure if it's always a good idea for Pleco to ask users to take tone changes into account when entering tones in flashcard tests. A user should know both the lexical tone of each syllable and the tone sandhi rules, which are quite simple to internalize and shouldn't really be practiced by entering them into a smartphone, but instead by pronouncing them. If Pleco asks for the tone as it's spoken, there's a definite risk that a user won't learn the actual, lexical tone properly. Also in cases like the following, it would quickly get a little impenetrable, especially for new users, if Pleco asked for the changed tone:
- Tone changes of 一 yī, where the first tone can sometimes turn into a second, and sometimes into a fourth tone
- Series of tone changes, such as 我很好！, where both the 我 and the 很 have their tone changed from third to second.
More importantly, it may not be all that easy to program. What if you have four third tones lexically, then Pleco would have to change three syllables' tones, which usually isn't right. It can quickly get a little complicated for a user to understand clearly whether a syllable's tone has changed or whether that's its original.
In addition, the real-life tone changes are often more complicated than the relatively simple tone sandhi rules we find in most textbooks. So it may be teaching you something simple which is actually wrong (or strangely super-correct) in many cases. A new grammar book by Jeroen Wiedenhof, which breaks with principles posited by many grammars, details this, as well:
Of course, it's still a matter of personal preference, and Pleco could also add an option for it. But when we don't want to do that, I feel that asking for lexical tones is the safer route.
In the case of longer expressions in dictionaries, it commonly happens that tone changes are incorporated in the expression. In this case Pleco would already ask for those changed tones, and there it makes more sense than in the case of disparate words put together.
Cheers, and good studying,