Because the kabbalists hold that it is a segulah to ward off the plague there seems to be a lot of emphasis being placed these days on reciting ketores as part of korbanos or after davening . The Rambam in Moreh Nevuchim (3:45) actually gives a far more mundane reason for the offering of ketores in Beis haMikdash: the sweet fragrance of ketores was needed to help overcome the stench of the animals that had to be butchered to offer korbanos.
The Rishonim already have problems with the Rambam's view. Meshech Chochma argues in their favor against the Rambam based on the pesukim in Pekudei.
Back in P' Titzaveh, when first describing the mizbach ha'ketores, the Torah describes its location as "lifnei ha'paroches" (30:6):
וְנָֽתַתָּ֤ה אֹתוֹ֙ לִפְנֵ֣י הַפָּרֹ֔כֶת
Similarly, at the end of our parsha (40:26):
וַיָּ֛שֶׂם אֶת־מִזְבַּ֥ח הַזָּהָ֖ב בְּאֹ֣הֶל מוֹעֵ֑ד לִפְנֵ֖י הַפָּרֹֽכֶת:
Yet earlier in that same perek, when describing the hakamas haMishkan, the Torah writes (40:5):
וְנָֽתַתָּ֞ה אֶת־מִזְבַּ֤ח הַזָּהָב֙ לִקְטֹ֔רֶת לִפְנֵ֖י אֲר֣וֹן הָֽעֵדֻ֑ת
Why the switch here to "lifnei aron ha'eidus?"
Meshech Chochma answers that the Torah here is not describing the location of the mizbach ha'ketores, but rather alluding to its function. It is not merely there as a perfume bottle, but rather just as the aron is a vehicle for hashra'as haShechina, so too, the offering of ketores is a means to bring hashara'as haShechina to the Mikdash.