Would this raise concerns as a red flag in my application? Has anyone applied under similar circumstances?
It likely would raise a red flag, yes. That said: red flags are perhaps more like yellow cards in football (soccer) - they don't eject you from the game (taken individually anyway), they are warnings to the officers to check more.
Your specific situation - effectively a small wedding without the traditional larger reception - may not be fatal to your app given other factors - some of which I do not know. It might be a more serious problem to an arranged marriage (which yours does not appear to be?).
Some other points or factors that may influence:
-your plans to have wedding reception in future are at best zero or only very slightly positive to your app (to point where it may not even be helpful to mention them in your app, although I don't know). The reason is that this "have a small often civil wedding without the other traditional trappings" approach seems to be interpreted by IRCC as "we didn't have a real wedding" (by local traditions, and of course can be cancelled easily) - and likely interpreted that way because it fits a pattern for fraudulent marriage apps. Often, it seems, fatal to arranged-marriage apps - perhaps not for other apps, but not much of a positive either. (*My language here may be overly negative - I mean 'fatal' only in the sense of 'resulting in a refusal.)
-how much time you spent together physically over the years, and esp after marriage, will be important. (Travel time alone together with physical evidence eg photos from before the marriage also good)
-does your spouse also live abroad (not in India)? Study / univrsity background / travel experience significant (outside India)?
-Did the guests at your wedding include close family, such as - esp - parents?
-Other general evidence of widespread knowledge of the wedding incl photos with friends and family?
Overall I'd say there is some evidence of spousal apps with smaller and even civil weddings being successful when it's quite clear from history of both that not an arranged marriage, 'secular' relationship and lifestyle, etc. (An example profile - not that uncommon - might be two professionals with advanced degrees who both studied and worked abroad and/or are living abroad). And of course there's everything in between.
You'll have to use your own judgment on whether to apply now. You might also want to strengthen the application in key ways, read through the app and see what it asks for in terms of evidence. An example might be if you have travel planned soon to spend time together, travel soon and include that time together, apply after returning.