IMHO, when natively portable versions concur with portabilized versions, the last ones should be listed as alternatives, for two reasons:
1) PortableApps.com has its own site. When redirected to there, the concerned user will find all the information that he/she needs, not only about some specific app, but about the whole project and its benefits, as long as other portabilized software taht are not listed in TPFC. (The same aplies to WinPenPack's portabilized software).
2) The installation procedure of PortableApps.com packages is simple and, even more importantly, standardized. Launch the .paf file and follow the instructions, no more than that is needed. When you do it once you are able to easily install every software packed in the PA.c format. (The same aplies to WinPenPack's portabilized software).
On the other hand, there's a wide range of procedures to install a natively portable application, from the simplest (unzip and run) to the more complex (uniextract, create .ini files with x content, rename the executable, etc.).
Taking into account that is not possible to know in advance which one is the correct for each case, and sometimes the information about how to make an application behave natively portable is really difficult to find, becomes natural to dedicate more space to better inform those visitors who are most in need, regardless of the virtues of each portable version (native or portabilized)
So, is not a question of personal preferences, but convenience and to assure a better service.
In this case in particular, since there is an attempt to discard this 7z package version in favour of the PA.c format, I think is better to wait a reasonable lapse to see the results.