Can I run a single Magento for CZ + SK cross-border?

Yes, CZ + SK is one of the cleanest cross-border setups in Europe because the markets share so much culture, language, and infrastructure:

• One Magento backend, 2 stores, yourbrand.cz + yourbrand.sk, shared catalogue, separate URLs.
• Per-store DPH, CZ 21% / 15% / 10%, SK 23% / 19% / 5%. Magento tax_zone rules per store.
• Per-store currency, CZ uses CZK (Kč), SK uses EUR (joined eurozone 2009). Magento currency-per-store handles this natively.
• Shared marketplaces, Heureka.cz + Heureka.sk, Aukro.cz + Aukro.sk. Same XML feed, two endpoints. Big advantage over building two separate stacks.
• Per-store payment, GoPay handles both, Tatra Pay / Slovenska Sporitelna buttons added on the SK side, ComGate is CZ-only.
• Per-store shipping, Zasilkovna / Packeta works across both (the dominant pickup-point carrier). PPL CZ for CZ, GLS for SK.

Czech and Slovak are mutually intelligible, most CZ shops just present Slovak as a second language toggle (cs_CZ + sk_SK locale codes), shared product copy. Saves 30%+ vs running two separate stacks.