This seems to be based on a misunderstanding of the Mishnah in Chagigah. Rashi explains "what is above" to mean:
מה למעלה - מרקיע שעל ראשי החיות:
Above the firmament which is above the heads of the Chayos
If Gehennom is below the Chayos but above the sky, there's no prohibition involved.
In a similar vein, the Maharsha on the spot understands this Gemara somewhat metaphorically:
גיהנם למעלה מן הרקיע וי״א כו׳. נראה ע״פ מ״ש בפרק אין דורשין בז׳ רקיעים מכון שבו אוצרות שלג כו׳ סופה וסערה כו׳ כל אלה לפורענות כפרש״י ופריך דבארעא איתנהו דכתיב שלג ומישור רוח סערה וגו׳ ומשני דוד הורידן שנאמר לא יגור במגורך רע והשתא הכא דקאמר למעלה מן הרקיע שכן היה שכל פורענות דגיהנם למעלה במכון היה וי״א לאחורי הרי חושך היינו לאחר שהורידן דוד וק״ל:
It appears according to that which they said in Ein Dorshin [second Perek of Chagigah], that in the seven firmaments are the storehouses for snow, etc., storm, etc., All of these are for punishment, as Rashi explains. It asks that these are in the ground, as it says, "Snow and smoke, storm wind, etc." and answers that David brought them down, as it says, "Evil will not dwell in Your dwelling place." Now, here, where it says that [Gehennom] is above the sky, it's because all the punishments of Gehennom were above in their abode. "And some say beyond the mountains of darkness" - that's after David brought them down.
Like the above interpretation, if the storehouses are in the lower firmaments, then they are not in violation of the Mishnah by discussing them.
I assume in this answer that all relevant Gemaras are meant literally. If, for instance, Gehennom is not literally above the sky, but rather the Beis Midrash of Eliyahu are employing a metaphor for something, then of course the question is moot.