Are Flipkart items reliable and original?

You can be sure that the items sold on Flipkart are original. However, you can ensure the following points being taken care of.
Please note that Flipkart never sells you products directly. They have registered sellers on their website who list the products with Flipkart. In the case of Flipkart, the preferred seller would be W S Retail. Make sure you are buying a product from such "Official" and "reliable" sellers.
Some of the products are shipped by Flipkart while a few are shipped by the individual sellers. Make sure you buy those products that are available in the warehouses. Such shipments are handled by Flipkart themselves. Such products are marked with the tag Flipkart Advantage.
Buying from sellers who have higher rating would be advisable to avoid any kind of fraud. Look for a seller rating of at least four stars. Also, check how many transactions have they handled.
However, please note that you are comparing an army store with a regular store. I do not think it should be practical in any way. The regular stores can never compete with the army stores in terms of pricing. The army stores get the products for a price lesser than the wholesalers. The E-commerce sites may come closer to the army stores as they source their products directly from the manufacturers or distributors.
If you really want to compare the prices, it would be a better idea to compare among the different online portals. But, you can be sure that the products sold on the site are genuine. Just make sure you go by the brand.

The price displayed on Flipkart (with official store name WS_RETAIL) or Amazon Inc has it on their pages, includes local taxes and delivery prices. So basically they are adding price to the wholesalers price.

Flipkart, amazon and Snapdeal does have original and reliable products. However scenario here refers a comparison with army store.

Army canteen or army store has specific wholesaler discount which makes the price of the product lower than the normal citizens. So on that point you can't compare the normal store price with the army store. My uncle used to work in AFMC office and they used to get such big discount from that store. And we used to compare the price with local stores. I think it'd be unfair for local store and also with Flipkart or Amazon for such comparison.

If we compare the same product with Flipkart or Amazon, then you'd find that normal stores can't offer same price as that of army stores.

No amount of Flipkart original or amazon original stores can be price matched with Army store (or navy and air force) for that matter can be compared with civilian stores.

Flipkart and amazon both have individual sellers and amazon blocks the sellers who sell fake or unreliable products. So they are bound to serve the quality. But price matching can't be used as a scale to judge their reliable and originality.

Items sold in Flipkart are reliable and original in most of the cases. I said in most of the cases because the seller from whom you are buying may fraud you and to avoid this, it is best to pick out sellers having good rating rather than sellers who are providing at the cheap price.

Army canteen items aren't inclusive of tax, so they get much lesser price than a normal store. They are cases where Flipkart trying to increase the price and then provide discount for that to attract customers rather than these there are no more issues from them.

As above said by the expert, Flipkart never sell most of the items directly to their customers who booked via online source / website. Most of the items are booked online by the customers which re-routed or copied to the associated seller where they get the notification and action upon. The only thing you get to go ahead is, ordering and paying to FK wherein as turn they get their commission and transaction follow up first and the rest go to correspondence seller.

The seller ensure that the product is delivered within the committed duration or else they would notify whether the product is available or not. However, most of the products from sellers are reliable except handloom items wherein some quality may arise subject to distributors or region wise or one can't confirm the brand.

In your case, yes, those shoes can be sold to lesser price just because of Flipkart's direct contact with manufacturer or main dealer, so, they get enough lesser or cost price and profit accordingly. The sales is depend on flows of the product, the more flows of the product the more chances of lesser price beside direct business contacts with manufacturer or main supplier. On the other hand, the rare selling product comes with good discount price too.